Design of bacteriophage-based artificial viruses for human genome remodeling

ABSTRACT

Described is an “artificial virus” (AV) programmed with biomolecules that can enter human cells and carry out precise human genome modification. The AVs comprise: at least one viral vector, such as bacteriophage T4; at least one therapeutic molecule, such as DNA, RNA, protein and their complex; and a lipid coating. Also described is a method of human genome modification, using such an AV, and a method of program such an AV.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation in part of claims benefit of priority of U.S. patent application Ser. No. 16/990,289, entitled “Prokaryotic-Eukaryotic Hybrid Viral Vector for Delivery of Large Cargos of Genes and Proteins into Human Cells,” filed Aug. 11, 2020, which claims benefit of priority of U.S. Provisional Patent Application No. 62/888,576 filed on Aug. 19, 2019, entitled “A Prokaryotic-Eukaryotic Hybrid Viral Vector for Delivery of Large Cargos of Genes and Proteins into Human Cells”. This application also claims benefit of priority of U.S. Provisional Patent Application No. 63/058,012, entitled “Design of Bacteriophage-based Artificial Viruses for Human Genome Remodeling,” filed Jul. 29, 2020. The entire contents and disclosures of these patent applications are incorporated herein by reference in their entirety.

GOVERNMENT INTEREST STATEMENT

This invention was made with the United States government support under Grant Nos. AI111538 and AI081726 awarded by The National Institutes of Health (NIH) and Grant No. MCB-0923873 awarded by The National Science Foundation (NSF). The government has certain rights in the invention.

REFERENCE TO A “SEQUENCE LISTING”

The present application includes a Sequence Listing which has been submitted electronically in an ASCII text format. This Sequence Listing is named 109007-23787US01_sequence listing.TXT was created on Jun. 7, 2021, is 51,445 bytes in size and is hereby incorporated by reference in its entirety.

BACKGROUND Field of the Invention

The present disclosure relates to generally to a human genome remodeling components, compositions, mechanisms and methods thereof.

BACKGROUND OF THE INVENTION

Designing “artificial viruses” (AVs) programmed with biomolecules that can enter human cells and carry out precise molecular repairs will have broad applications to medicine. However, formulating an AV particle that can efficiently and safely deliver both therapeutic genes and proteins into the target cell to remodel human genome is still a major challenge. The present application overcomes the shortcomings of the prior art as described herein.

SUMMARY

According to a first broad aspect, the present disclosure provides a human genome remodeling artificial virus (AV) comprising: at least one viral vector; at least one therapeutic molecule; and a lipid coating, wherein at least one of the therapeutic molecules has gene modification or gene silencing activities.

According to a second broad aspect, the present disclosure provides a human genome remodeling artificial virus (AV) comprising: a T4 capsid; Cas9 protein; at least one RNA; at least one DNA; and a lipid coating, wherein the DNA is packaged inside the T4 capsid, wherein the RNA is selected from the group consisting of mRNA, siRNA and gRNA, wherein the lipid coating comprises at least one cationic lipid.

According to a third broad aspect, the present disclosure provides a method of genome modification comprising: infecting animal cells with an artificial virus (AV), wherein the AV comprises a viral vector; at least one therapeutic molecule; and a lipid coating, wherein at least one of the therapeutic molecules has gene modification or gene silencing activities.

According to a fourth broad aspect, the present disclosure provides a CRISPR-based method of programming artificial virus (AV) with genome modification capabilities comprising: generating a “acceptor” phage by deleting ipI and ipII genes from a wild type T4 phage; generating a host bacteria cell with a plasmid containing a gene of target protein and a spacer plasmid that expresses Cas9 or Cpf1 and CRISPR RNA corresponding to a protospacer sequence in the deleted region of the acceptor phage; infecting the host bacteria cell with the “acceptor” phage; recovering an engineered “acceptor” phage from the host bacteria cell; obtaining an empty engineered T4 capsid from the engineered “acceptor” phage; packaging at least one DNA in the engineered T4 capsid, wherein the gene of target protein is flanked by capsid targeting sequence (CTS) at the C-terminus and nuclear localization sequence (NLS) at the N-terminus to form CTS-gene-NLS sequence.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the office upon request and payment of the necessary fee.

The accompanying drawings, which are incorporated herein and constitute part of this specification, illustrate exemplary embodiments of the invention, and, together with the general description given above and the detailed description given below, serve to explain the features of the invention.

FIG. 1 is a schematic diagram of the bacteriophage T4-based artificial viruses according to one exemplary embodiment of the present invention.

FIG. 2 is a schematic diagram of sequential assembly-line to generate T4-AVs according to one exemplary embodiment of the present invention.

FIG. 3 is a graph showing the lipid-coated T4-AVs according to one embodiment of the present invention.

FIG. 4 is a graph showing the quantification of packaged GFP and luciferase DNAs for various T4-AVs at different DNA to T4 ratio according to one exemplary embodiment of the present invention.

FIG. 5 is a graph showing the delivery of packaged DNA by T4(GFP)-AVs into 293 cells at different multiplicity of infection (MOI) according to one exemplary embodiment of the present invention.

FIG. 6 is a graph showing the effect of T4 and lipid complexation volume on DNA delivery efficacy according to one exemplary embodiment of the present invention.

FIG. 7 is a graph showing the effect of T4 and lipid complexation time on DNA delivery efficacy according to one exemplary embodiment of the present invention.

FIG. 8 is a graph showing the transduction efficiencies of AVs coated with different cationic lipids according to exemplary embodiments of the present invention.

FIG. 9 is a graph showing the optimal ratio of T4 head particles to LPF2K concentration on delivery efficacy and cell viability according to one exemplary embodiment of the present invention.

FIG. 10 is a graph showing the optimal ratio of T4 head particles to LPF2K concentration on delivery efficacy and cell viability according to one exemplary embodiment of the present invention.

FIG. 11 is a graph showing the quantification of packaged VRCO1 plasmid for T4-AVs at different DNA to T4 ratio according to one exemplary embodiment of the present invention.

FIG. 12 is a graph showing the quantification of the amount of VRCO1 antibody secreted by transduced cells according to one exemplary embodiment of the present invention.

FIG. 13 is a graph showing the quantification of packaged VRC01 and CH58 plasmids for T4-AVs at different DNA to T4 ratio according to one exemplary embodiment of the present invention.

FIG. 14 is a graph showing the quantification of the amount of VRCO1 and CH58 antibodies secreted by transduced cells according to one exemplary embodiment of the present invention.

FIG. 15 is a graph showing the comparison of transduction efficiencies of T4-AVs and AAVs according to one exemplary embodiment of the present invention.

FIG. 16 is a graph showing the comparison of luciferase expression with the presence of different compounds according to one exemplary embodiment of the present invention.

FIG. 17 is a graph showing the comparison of GFP expression with the presence of different compounds according to one exemplary embodiment of the present invention.

FIG. 18 is a graph showing the enhancement of T4-AV delivery with TBA treatment according to one exemplary embodiment of the present invention.

FIG. 19 is a schematic diagram showing the locations of protein and DNA cargos carried by T4-AVs according to one exemplary embodiment of the present invention.

FIG. 20 is a graph showing the display of β-Gal-Soc on T4 capsids according to one exemplary embodiment of the present invention.

FIG. 21 is a graph showing the display of Cre-Hoc on T4 capsids according to one exemplary embodiment of the present invention.

FIG. 22 is a graph showing the display of various Soc- and Hoc-fused proteins on T4 capsids according to one exemplary embodiment of the present invention.

FIG. 23 is a graph showing the quantification of packaged mCherry reporter plasmid for T4-AVs at different DNA to T4 ratio according to one exemplary embodiment of the present invention.

FIG. 24 is a graph showing the internalization of GFP protein and expression of mCherry DNA according to one exemplary embodiment of the present invention.

FIG. 25 is a graph showing the internalization of GFP protein at 3 h after treatment according to one exemplary embodiment of the present invention.

FIG. 26 is a graph showing the expression of mCherry DNA according to one exemplary embodiment of the present invention.

FIG. 27 is a graph showing β-galactosidase enzyme activity and GFP expression according to one exemplary embodiment of the present invention.

FIG. 28 is a graph showing comparison of T4-AV delivery using various displayed proteins according to one exemplary embodiment of the present invention.

FIG. 29 is a graph showing transduction of TAT-displayed T4-AVs at different copy numbers of TAT per capsid and at different MOI according to one exemplary embodiment of the present invention.

FIG. 30 is a graph showing increased delivery efficiency of T4(GFP)-AVs into 293 cells with Soc-TAT decoration according to one exemplary embodiment of the present invention.

FIG. 31 is a graph showing enhanced transduction by T4-AVs displayed with integrin-binding RGD motif according to one exemplary embodiment of the present invention.

FIG. 32 is a schematic diagram showing expression and purification of NLS-Cas9 and NLS-Cas9-Soc according to one exemplary embodiment of the present invention.

FIG. 33 is a graph showing the quantification of Cas9-Soc (SEQ ID NO: 16) displayed on T4 capsid according to one exemplary embodiment of the present invention.

FIG. 34 is a graph showing the quantification of packaged gRNA for T4-AVs according to one exemplary embodiment of the present invention.

FIG. 35 is a microscopy image showing enhanced GFP reporter expression according to one exemplary embodiment of the present invention.

FIG. 36 is a graph showing the formation of Cas9-gRNA ribonucleoprotein (RNP) complexes according to one exemplary embodiment of the present invention.

FIG. 37 is a graph showing the gRNA-directed cleavage of target DNA according to one exemplary embodiment of the present invention.

FIG. 38 is a graph showing the disruption of endogenous AAVS1 locus according to one exemplary embodiment of the present invention.

FIG. 39 is a graph showing the efficiency of genome editing according to one exemplary embodiment of the present invention.

FIG. 40 is a schematic diagram showing genome editing AVs according to one exemplary embodiment of the present invention.

FIG. 41 is an EM photo showing the presence of genome editing complexes decorating the Capsid according to one exemplary embodiment of the present invention.

FIG. 42 is a graph showing the binding of gRNA to T4(GFP)-Soc-Cas9 capsids increases with increasing ratios of gRNA molecules to Soc binding sites according to one exemplary embodiment of the present invention.

FIG. 43 is a graph showing the binding of gRNA to T4(GFP)-Soc-Cas9 increases by increasing the ratio of Cas9-Soc molecules to Soc binding sites according to one exemplary embodiment of the present invention.

FIG. 44 is a graph showing the impact of binding of gRNA to T4(GFP)-Soc-Cas9 on the display of Cas9-Soc on T4 according to one exemplary embodiment of the present invention.

FIG. 45 is a graph showing the comparison of luciferase activity in cells treated with T4(Luci)-AVs or T4(Luci)-Soc-Cas9-gRNA-AVs at increasing gRNA binding ratio according to one exemplary embodiment of the present invention.

FIG. 46 is a graph showing representative fluorescence images of cells treated with T4(GFP)-Soc-Cas9-AVs and T4(GFP)-Soc-Cas9-gRNA-AVs according to one exemplary embodiment of the present invention.

FIG. 47 is a graph showing the genome editing at the AAVS1 locus by RNP-AVs delivered at different ratios of AV nanoparticles to cells according to one exemplary embodiment of the present invention.

FIG. 48 is a graph showing the comparison of AAVS1 indel efficiencies using T4-AVs in different configurations according to one exemplary embodiment of the present invention.

FIG. 49 is a graph showing HBB gene disruption mediated by T4(GFP)-Soc-Cas9-HBBgRNA-AVs according to one exemplary embodiment of the present invention.

FIG. 50 is a graph showing simultaneous genome editing at two target sites on human genome by T4-AVs according to one exemplary embodiment of the present invention.

FIG. 51 is a schematic diagram showing the design of AV-mediated genome editing and homologous recombination at the AAVS1 locus according to one exemplary embodiment of the present invention.

FIG. 52 is a graph showing the quantification of packaged puromycin plasmid DNA for T4-AVs according to one exemplary embodiment of the present invention.

FIG. 53 is a graph showing the PCR assay on puromycin resistant single cell clones following transduction with T4(Puro-donor)-Soc-Cas9-gRNA-AVs according to one exemplary embodiment of the present invention.

FIG. 54 is a graph showing DNA sequencing of the PCR amplicon confirming the presence of puromycin donor insertion at the target site in each of the clones according to one exemplary embodiment of the present invention.

FIG. 55 is a schematic diagram showing the locations of PCR amplification primer sets for detecting targeted insertions according to one exemplary embodiment of the present invention.

FIG. 56 is a graph showing the detection of amplified sequences according to one exemplary embodiment of the present invention.

FIG. 57 is a schematic diagram showing the site-specific recombination by delivery of Cre-Hoc-T4(LSL-GFP+mCherry)-Soc-Cas9-gRNA-AVs according to one exemplary embodiment of the present invention.

FIG. 58 is a schematic diagram showing the Cre-Hoc expression cassette according to one exemplary embodiment of the present invention.

FIG. 59 is a graph showing the size-exclusion chromatography profile of Cre-Hoc protein according to one exemplary embodiment of the present invention.

FIG. 60 is a graph showing the site-specific recombination activities of Cre-Hoc according to one exemplary embodiment of the present invention.

FIG. 61 is a graph showing co-display of Cas9-Soc and Cre-Hoc according to one exemplary embodiment of the present invention.

FIG. 62 is a graph showing the impact of Cre-Hoc binding on the binding of Cas9-gRNA RNP on the same capsid according to one exemplary embodiment of the present invention.

FIG. 63 is a graph showing the quantification of packaged LSL-GFP plasmid DNA for T4-AVs according to one exemplary embodiment of the present invention.

FIG. 64 is a graph showing the co-delivery and co-expression of LSL-GFP and mCherry DNAs according to one exemplary embodiment of the present invention.

FIG. 65 is a graph showing the representative GFP expression images following transduction of 293 cells with Cre-Hoc-T4(LSL-GFP)-Soc-Cas9-gRNA-AVs at increasing Cre-Hoc display ratio according to one exemplary embodiment of the present invention.

FIG. 66 is a schematic diagram showing the delivery of Cre-Hoc-T4(Luci)-Soc-Cas9-gRNA-AVs into Cre reporter cells according to one exemplary embodiment of the present invention.

FIG. 67 is a graph showing the AVs mediated efficient site-specific recombination in Cre reporter cells according to one exemplary embodiment of the present invention.

FIG. 68 is a graph showing the luciferase activity and AAVS1 indel frequencies of the cells treated with Cre-Hoc-T4(Luci)-RNP-AVs at increasing Cre-Hoc display ratios according to one exemplary embodiment of the present invention.

FIG. 69 is a graph showing the stoichiometry of gRNA/siRNA:Cas9-Soc binding according to one exemplary embodiment of the present invention.

FIG. 70 is a schematic diagram showing the T4-AVs carrying siRNA and mRNA payloads according to one exemplary embodiment of the present invention.

FIG. 71 is a graph showing the binding of siRNA to the T4(gRNA-GFP)-Soc-Cas9 capsids at increasing ratios of siRNA molecules to Soc binding sites according to one exemplary embodiment of the present invention.

FIG. 72 is a graph showing the effect of siRNA:T4(Luci)-Soc-Cas9 ratios on the AV delivery efficiency according to one exemplary embodiment of the present invention.

FIG. 73 is a graph showing the silencing of GFP expression in 293 cells treated with GFPsiRNA-AVs according to one exemplary embodiment of the present invention.

FIG. 74 is a graph showing the quantification of GFP protein levels by GFPsiRNA-AVs at 48 and 72 h post-transduction according to one exemplary embodiment of the present invention.

FIG. 75 is a graph showing the effect of the displayed siRNA amount on the efficiency of GFP gene silencing according to one exemplary embodiment of the present invention.

FIG. 76 is a graph showing simultaneous gene silencing at two sites by incorporating two siRNAs into the same AV according to one exemplary embodiment of the present invention.

FIG. 77 is a graph showing the loading of GFPmRNA on T4(mCherry)-Soc-Cas9 capsids at increasing ratios of mRNA molecules to Soc binding sites according to one exemplary embodiment of the present invention.

FIG. 78 is a graph showing the binding of mRNA to Cas9-Soc protein at increasing ratios of Cas9-Soc molecules to mRNA according to one exemplary embodiment of the present invention.

FIG. 79 is a graph showing co-localization of gene expression of AV-packaged mCherry plasmid DNA and AV-displayed GFP mRNA in the same cell. according to one exemplary embodiment of the present invention.

FIG. 80 is a graph showing the delivery and expression of AV(mCherry) as a control according to one exemplary embodiment of the present invention.

FIG. 81 is a graph showing the impact of the amount of displayed mRNA on the co-delivery efficiency of T4(Luci)-Soc-Cas9-mRNA-AVs according to one exemplary embodiment of the present invention.

FIG. 82 is a graph showing the quantification of packaged gRNA expression plasmid for various T4-AVs according to one exemplary embodiment of the present invention.

FIG. 83 is a graph showing the replacement of bound siRNA in the Cas9-siRNA complex by gRNA according to one exemplary embodiment of the present invention.

FIG. 84 is a graph showing the quantification of AAVS1 indel frequencies of cells treated with T4(AAVS1gRNA-GFP)-Soc-Cas9-siRNA-AVs at increasing ratios of siRNA molecules to soc binding sites according to one exemplary embodiment of the present invention.

FIG. 85 is a graph showing the genome editing at AAVS1 locus by T4(AAVS1gRNA-mCherry)-Soc-Cas9-GFPmRNA-AVs at increasing ratios of mRNA molecules to capsid-displayed Cas9 according to one exemplary embodiment of the present invention.

FIG. 86 is a schematic diagram showing the programmable guided transport system (GIS) using CRISPR-engineered T4-AVsaccording to one exemplary embodiment of the present invention.

FIG. 87 is a schematic diagram showing the CRISPR-mediated CLN gene insertion according to one exemplary embodiment of the present invention.

FIG. 88 is a graph showing the CRISPR-mediated T4 genome editing according to one exemplary embodiment of the present invention.

FIG. 89 is a graph showing the size-exclusion chromatography profile according to one exemplary embodiment of the present invention.

FIG. 90 is a graph showing the expression of head-packaged CLN protein according to one exemplary embodiment of the present invention.

FIG. 91 is a graph showing functional characterizations of CLN protein and T4(CLN) heads according to one exemplary embodiment of the present invention.

FIG. 92 is a graph showing enhanced laco-luciferase DNA delivery by T4(CLN)-GIS-AVs at different ratios of AVs to cells according to one exemplary embodiment of the present invention.

FIG. 93 is a graph showing enhanced genome editing by T4(CLN)-GIS-AVs according to one exemplary embodiment of the present invention.

FIG. 94 is a graph showing biochemical characterization of GFP-packaged AVs according to one exemplary embodiment of the present invention.

FIG. 95 is a graph showing biochemical characterization of Cre-packaged AVs according to one exemplary embodiment of the present invention.

FIG. 96 is a graph showing the formation of functional β-galactosidase tetramers according to one exemplary embodiment of the present invention.

FIG. 97 is a graph showing size-exclusion chromatography profile of T4(GFP) capsid according to one exemplary embodiment of the present invention.

FIG. 98 is a graph showing fluorescence images of “Green fluorescence phage” according to one exemplary embodiment of the present invention.

DETAILED DESCRIPTION OF THE INVENTION Definitions

Where the definition of terms departs from the commonly used meaning of the term, applicant intends to utilize the definitions provided below, unless specifically indicated.

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood to which the claimed subject matter belongs. In the event that there is a plurality of definitions for terms herein, those in this section prevail. All patents, patent applications, publications and published nucleotide and amino acid sequences (e.g., sequences available in GenBank or other databases) referred to herein are incorporated by reference. Where reference is made to a URL or other such identifier or address, it is understood that such identifiers can change and particular information on the internet can come and go, but equivalent information can be found by searching the internet. Reference thereto evidences the availability and public dissemination of such information.

It is to be understood that the foregoing general description and the following detailed description are exemplary and explanatory only and are not restrictive of any subject matter claimed. In this application, the use of the singular includes the plural unless specifically stated otherwise. It must be noted that, as used in the specification and the appended claims, the singular forms “a,” “an” and “the” include plural referents unless the context clearly dictates otherwise. In this application, the use of “or” means “and/or” unless stated otherwise. Furthermore, use of the term “including” as well as other forms, such as “include”, “includes,” and “included,” is not limiting.

For purposes of the present disclosure, the term “comprising”, the term “having”, the term “including,” and variations of these words are intended to be open-ended and mean that there may be additional elements other than the listed elements.

For purposes of the present disclosure, directional terms such as “top,” “bottom,” “upper,” “lower,” “above,” “below,” “left,” “right,” “horizontal,” “vertical,” “up,” “down,” etc., are used merely for convenience in describing the various embodiments of the present disclosure. The embodiments of the present disclosure may be oriented in various ways. For example, the diagrams, apparatuses, etc., shown in the drawing figures may be flipped over, rotated by 90° in any direction, reversed, etc.

For purposes of the present disclosure, a value or property is “based” on a particular value, property, the satisfaction of a condition, or other factor, if that value is derived by performing a mathematical calculation or logical decision using that value, property or other factor.

For purposes of the present disclosure, it should be noted that to provide a more concise description, some of the quantitative expressions given herein are not qualified with the term “about.” It is understood that whether the term “about” is used explicitly or not, every quantity given herein is meant to refer to the actual given value, and it is also meant to refer to the approximation to such given value that would reasonably be inferred based on the ordinary skill in the art, including approximations due to the experimental and/or measurement conditions for such given value.

For purposes of the present invention, the term “bacterial viruses”, “bacteriophages”, and “phages” are used interchangeably. These terms refer to a virus or a viral particle that can infect bacteria.

For purposes of the present invention, the term “capsid” and the term “capsid shell” refer to the protein shell of a virus comprising several structural subunits of proteins. The capsid encloses the nucleic acid core of the virus.

For purposes of the present invention, the term “vector”, “vehicle”, and “nanoparticle” are used interchangeably. These terms refer to a virus or a hybrid viral particle that can be used to deliver genes or proteins.

For purposes of the present invention, the term “bind,” the term “binding” and the term “bound” refer to any type of chemical or physical binding, which includes but is not limited to covalent binding, hydrogen binding, electrostatic binding, biological tethers, transmembrane attachment, cell surface attachment and expression.

For purposes of the present invention, the term “nucleic acid” refers to polymers of nucleotides of any length, and include DNA and RNA. The nucleic acid bases that form nucleic acid molecules can be the bases A, C, G, T and U, as well as derivatives thereof. Derivatives of these bases are well known in the art. The term should be understood to include, as equivalents, analogs of either DNA or RNA made from nucleotide analogs. The term should also be understood to include both linear and circular DNA. The term as used herein also encompasses cDNA, that is complementary, or copy, DNA produced from an RNA template, for example by the action of reverse transcriptase.

For purposes of the present invention, the term “neck protein” and the term “tail protein” refer to proteins that are involved in the assembly of any part of the necks or tails of a virus particle, in particular bacteriophages. Tailed bacteriophages belong to the order Caudovirales and include three families: The Siphoviridae have long flexible tails and constitute the majority of the tailed viruses. Myoviridae have long rigid tails and are fully characterized by the tail sheath that contracts upon phage attachment to bacterial host. The smallest family of tailed viruses are podoviruses (phage with short, leg-like tails). For example, in T4 bacteriophage gp10 associates with gpll to forms the tail pins of the baseplate. Tail-pin assembly is the first step of tail assembly. The tail of bacteriophage T4 consists of a contractile sheath surrounding a rigid tube and terminating in a multiprotein baseplate, to which the long and short tail fibers of the phage are attached. Once the heads are packaged with DNA, the proteins gp13, gp14 and gp15 assemble into a neck that seals of the packaged heads, with gp13 protein directly interacting with the portal protein gp20 following DNA packaging and gp14 and gp15 then assembling on the gp13 platform. Neck and tail proteins in T4 bacteriophage may include but are not limited to proteins gp6, gp25, gp53, gp8, gp10, gp11, gp7, gp29, gp27, gp5, gp28, gp12, gp9, gp48, gp54, gp3, gp18, gp19, gp13, gp14, gp15 and gp63.

For purposes of the present invention, the term “MOI” and the term “multiplicity of infection” refer to the ratio of agents (e.g. phage or more generally virus, bacteria) to infection targets (e.g. cell). In the present disclosure, these terms refer to the ratio of “artificial virus” (AV) particles to the human cells infected.

For purposes of the present invention, the term “RNP” and the term “ribonucleoprotein” refer to a complex of ribonucleic acid and RNA-binding protein (e.g. the complex of Cas9 protein and RNA). Examples of RNA include gRNA, mRNA and siRNA.

For purposes of the present invention, the term “complexation volume” refer to the total volume of mixture, in which a reaction is carried out. For instance, the complexation volume is the total volume of T4 and lipid mixture, which can range from 10-400 μl, as shown in FIG. 6, when evaluating the impact of complexation volume on DNA delivery efficacy.

For purposes of the present invention, the term “complexation time” refer to the total reaction time, for which a reaction is carried out. For instance, the complexation time is the total amount of time, for which T4 and lipid are mixed in order for T4 to be coated by lipid, which can range from 5-120 min, as shown in FIG. 7, when evaluating the impact of complexation time on DNA delivery efficacy.

For purposes of the present invention, the term “N.S.” and the term “not significant” and the term “not significantly” refer to when the p value of Student's t-tests performed between two groups of data is less than 0.05.

For purposes of the present invention, the term “knock down” and the term “silencing” refer to a regulation of gene expression in a cell to prevent the expression of a certain gene. This regulation can occur through genetic modification or other treatment during either transcription or translation and is often used in research.

Description

While the invention is susceptible to various modifications and alternative forms, specific embodiment thereof has been shown by way of example in the drawings and will be described in detail below. It should be understood, however that it is not intended to limit the invention to the particular forms disclosed, but on the contrary, the invention is to cover all modifications, equivalents, and alternatives falling within the spirit and the scope of the invention.

Viruses are the most numerous and widely distributed organisms on Earth. They are also the most efficient biological machines³⁸. A single virus about 100 nm in size containing a genetic code of mere 10,000-30,000 nucleotides, such as HIV, influenza virus, or coronavirus, can impair or kill a human person consisting of about 37 trillion cells, each ˜100 um in size and carrying a genetic code of ˜3 billion nucleotides. This is because viruses evolved efficient mechanisms to replicate and assemble progeny on fast timescales, on the order of minutes in the case of bacterial viruses^(11,34). Hundreds to thousands of progeny viruses emerge from each infection, rapidly accumulating billions to trillions of new viruses starting from a single infection. This can cause global pandemics such as the current one caused by the novel coronavirus SARS-CoV-2⁵⁹. If some of the efficient viral mechanisms could be harnessed by building “artificial viruses” (AVs) in the test tube, programmed with therapeutic molecules, such viruses, instead of replicating in host, could perform beneficial tasks to restore human health. Depending on the biomolecules it is programmed with, an artificial virus could replace a defective gene with a functional gene (gene therapy), manufacture a therapeutic molecule (immunotherapy), kill a cancer cell (cancer therapy), and so on^(29,35,62). However, despite many attempts over the years, the concept of artificial viruses remained a theoretical possibility.

An alternative approach researchers have taken was to engineer natural human viruses such that they can deliver a piece of therapeutic DNA or RNA as part of their genome. Two types of viruses, lentiviruses with ˜10 Kbp size single-stranded RNA genome and adeno-associated viruses (AAVs) with ˜5 Kbp size single-stranded DNA genome have been extensively employed^(14,33). While this approach has been successful, it also has inherent limitations. These viruses at best can deliver 1 or 2 therapeutic genes and it is difficult to incorporate additional therapeutic molecules such as proteins or protein-nucleic acid complexes that are essential for complex molecular operations such as genome editing. Safety concerns due to broad infectivity to human cells, pre-existing immunity, toxicity, and potential integration into host genome pose serious concerns^(30,61).

In the present disclosure, a new type of artificial virus platform using the bacteriophage T4 is described. T4 belongs to myoviridae family and infects Escherichia coli bacterium, and it does not have any of the above limitations or safety concerns³¹. With an infection efficiency near 100%, and replicating at a rate of ˜20 minutes, T4 is one of the most efficient viruses known⁶⁰. FIG. 1 shows components of bacteriophage T4-based artificial viruses. Panel A of FIG. 1 shows structural model of phage T4 head (capsid), in which pentameric gp24* (124) vertices are shown in dark red. Panel B of FIG. 1 shows enlarged capsomer (hexamer), illustrating the arrangement of the major capsid protein gp23* (104) (dark green), Soc trimers (108) (light green), and Hoc fiber (106) (cyan). Panel C of FIG. 1 shows enlarged portal vertex showing gp20 (116) dodecamer (brown) and pentameric DNA packaging motor gp17 (118) (yellow). Panel D of FIG. 1 shows eight hundred and seventy Soc (108) molecules assembled at the quasi-three fold axes form a molecular cage (110) around the T4 capsid. Panel E of FIG. 1 shows one hundred and fifty-five Hoc fibers (112) from the center of capsomers. Panel F of FIG. 1 shows surface view of T4 capsid depicting the distribution of negative charges (114). Each negative charge is shown in red color.

As shown in FIG. 1, it contains a large 120×86 nm prolate icosahedral capsid (head) (122) assembled with 930 molecules or 155 hexameric capsomers (102) of 930 copies of the major capsid protein gp23* (104) (“*” represents cleaved mature form), 55 copies or 11 pentamers of gp24* (124) at eleven of the twelve vertices, and 12 copies of the portal protein gp20 (116) at the unique twelfth vertex5, 16, 34.

As shown in panel B of FIG. 1, each hexameric capsomers contains one copy of Hoc protein (106), 6 copies of gp23* (104) and 6 copies of Soc protein (108) that are shared with adjacent capsomers. Accordingly, each T4 head contains 155 copies of Hoc protein (106), 930 copies of gp23* (104) and 870 copies of Soc protein (108).

As shown in panel C of FIG. 1, attached to the twelfth vertex is the DNA packaging machine (126), containing 12 copies of the portal protein gp20 (116), and 5 copies of motor protein gp17 (118) and a central channel through which DNA of about 170 Kb (120) is transported. The portal vertex is a ring structure with a ˜35 Å central channel through which the viral genome is transported into capsid by an ATP-powered pentameric molecular motor attached to it^(15, 50). The molecular motor contains 5 copies of motor protein gp17 (118). After one headful of genome, equivalent to ˜170 Kbp linear dsDNA (120), is packaged^(4, 42), the motor dissociates and “neck” proteins assemble followed by tail and tail fiber assembly to generate an infectious virion^(26, 60).

The surface of T4 capsid is arrayed with two nonessential outer capsid proteins, Soc (108) (small outer capsid protein) (9.1 kDa; 870 copies per capsid) and Hoc (106) (highly antigenic outer capsid protein) (40.4 kDa; 155 copies per capsid)^(16, 21). Soc (108) is a tadpole-shaped molecule and binds at the quasi three-fold axes as a trimer. Each Soc (108) subunit acts as a “molecular clamp” by clasping two adjacent capsomers. As shown in panel D of FIG. 1, eight hundred and seventy such clamps form a molecular cage around the capsid greatly reinforcing the pressurized capsid due to its tightly packed DNA approaching crystalline density³⁹. Consequently, the capsid is very stable even under harsh conditions such as pH 11. Hoc (106) on the other hand is a 170 Å-long fiber containing a string of four Ig-like domains with the C-terminal domain bound to the center of each gp23* capsomer (102). One hundred and fifty-five symmetrically positioned Hoc fibers emanate from T4 head¹⁷. Unlike Soc, Hoc provides only marginal stability to capsid. Its main function might be to allow phage to adhere to host surfaces through its Ig-like domains¹.

There are many reasons why phage T4 is an ideal platform to build artificial viruses. In fact, this concept evolved over ˜40-years of genetic, biochemical, and structural analyses. First, the architecture of T4 phage with a stable capsid, external surface exposing 1,025 nonessential molecules, and an internal volume that can accommodate up to ˜170 Kbp DNA provide a large amount of cargo space to incorporate therapeutic biomolecules^(5, 54). Second, there is a rich amount of accumulated knowledge on the genetic and biochemical mechanisms of head assembly and genome packaging that allow in vitro manipulations to build artificial viruses9, 22, 41, 47. Third, the atomic structures of almost all the capsid and packaging motor components that provided a wealth of information to engineer the T4 nanoparticle have been determined^(5, 15, 17, 39, 49, 50). Fourth, a series of studies demonstrated that Soc and Hoc serve as excellent adapters to tether foreign proteins to T4 capsid surface^(27, 47). Both have nanomolar affinity and exhibit exquisite specificity to T4 capsid, properties that are critically important for in vitro assembly^(51, 65). Fifth, a robust in vitro DNA packaging system in which a stable “emptied” T4 capsid can be re-filled with foreign DNA using the powerful DNA packaging motor has been developed^(18, 63). Finally, a CRISPR engineering strategy has been developed recently, which allowed facile insertion of foreign DNA fragments into phage genome to generate recombinant phages with unique phenotypic properties^(44, 52, 53).

These provided an extraordinary foundation to design an artificial virus platform using T4 phage. The artificial virus design in the present disclosure takes an assembly-line approach, beginning with the empty capsid shell containing only three minimally essential capsid proteins gp23* (104), gp24* (124), and gp20 (116), and devoid of DNA and all other structural components including Soc, Hoc, neck, tail, and fibers. Using this protein shell as the basic building block, layers of cargo molecules are incorporated by a sequential process. Both the inside and outside of the shell are filled with these molecules that include proteins, DNAs, RNAs, and their complexes. The capsids are then coated with lipid molecules to create an “envelope” around these virus-like nanoparticles. The artificial viruses thus assembled mimic natural (human) viruses with a lipid coat, surface molecules, capsid shell, and packaged “genome”. As the exemplary embodiments and examples in the present disclosure would demonstrate, these artificial viruses appear to use similar pathways used by natural viruses for entry into cells and trafficking to intracellular destinations.

As proof of this concept, the assembly of a series of artificial viruses that are directed to perform specific molecular operations to remodel the human genome is demonstrated in the present disclosure. These include: genome editing, gene recombination, gene replacement, gene expression, and gene silencing. For example, in one configuration, an artificial virus was programmed with five different components; Cas9 genome editing nuclease, Cre recombinase, two gRNAs, donor, and reporter plasmids. These AVs entered human cells by endocytosis and delivered payload molecules in the cytosol, which, upon reaching the appropriate intracellular locations, performed genome editing and site-specific recombination at distinct sites on the human genome. Such a large capacity, all-in-one, multiplex, programmable, and phage-based artificial viruses represent a new category of nanomaterial that could potentially transform future human therapies and personalized medicine⁴⁸.

Assembly of Phage T4 Artificial Viruses

In one embodiment, the artificial viruses are assembled by sequential incorporation of purified biomaterials to generate a virus structural mimic, as shown in FIG. 2. Starting with an empty capsid shell (202) isolated from a neck- and tail-minus T4 phage mutant-infected E. coli ⁶³, a pentameric packaging motor (208) was assembled on the portal vertex by simply adding the (monomeric) motor protein gp17 (206) to the reaction mixture. The capsid interior is then filled with foreign DNA by adding linearized plasmid DNA and ATP to the assembly reaction (a, b in FIG. 2)⁵⁰. The T4 packaging motor (208) captures DNA (204) and translocates the DNA into capsid from one end to the other in a processive fashion. This can repeat many times resulting in successive packaging of a series of DNA molecules until the head is full (headful packaging)^(25, 56). Consequently, multiple copies of multiple plasmids are packaged inside the ˜170 Kbp capacity T4 head⁶³. The DNA packed T4 head (210) is shown in FIG. 2 after step b. Since the motor exhibits no sequence specificity, the composition of the packaged “genome” would be the same as that presented to the assembly reaction.

The exterior of the capsid was then arrayed with Soc- (212) and/or Hoc-fused protein (216) molecules by adding these proteins to the same reaction mixture (c, d in FIG. 2). The Soc-fused protein (212) may be Soc-protein or Soc-ribonucleoprotein (RNP). The Hoc-fused protein (216) is Hoc-protein combination. At ˜20:1 ratio of molecules to binding sites, full occupancy, i.e., up to 870 Soc- (212) and 155 Hoc-fused proteins (216) per capsid, can be achieved^(5, 51). The particles (214 and 218) coated with Soc- (212) and/or Hoc-fused protein (216) molecules are shown in FIG. 2., after steps c and d, respectively. The particles are then coated with cationic lipid molecules (220) (e in FIG. 2), resulting in the final artificial virus particle (222).

Since the T4 capsid has a high density of negative charges, ˜8,700 per capsid^(5,45), as shown in panel F of FIG. 1, cationic lipids would spontaneously assemble on T4 capsid via electrostatic interaction. In one embodiment, extensive lipid binding occurs when cationic lipids are added to T4 capsids. FIG. 3 contains microscopic photos showing the lipid (304) surrounding the T4 capsid (302). As shown in FIG. 3, a negative EM photo (306) shows a diffused stain (304), which is lipid, around the T4 capsid (302). When labeled with fluorophores, these “enveloped” particles (yellow, after combining Alexa Fluor 594 fluorophore and NBD fluorophore) (312) showed co-localization of the T4 capsid-labeled Alexa Fluor 594 fluorophore (red) (308) and the lipid-labeled NBD fluorophore (green) (310). The T4-AV nanoparticles thus assembled possess the basic architecture of naturally enveloped viruses with lipid coat, surface-exposed molecules, capsid shell, and packaged “genome”.

The T4 Artificial Viruses Efficiently Deliver Genetic Payloads into Human Cells

The T4-AVs by virtue of their positively charged lipid coat would efficiently bind to the negatively charged and lipophilic surface of human cells and allow efficient entry⁵⁷. Several cationic lipids and cell penetration peptides have been well-documented to exhibit such a property^(19, 66). Indeed, a series of embodiments in the present disclosure have demonstrated that the lipid-coated T4-AVs efficiently delivered genetic payloads into human cells.

In one embodiment, when co-packaged with two different plasmids, on average ˜5 molecules each of GFP reporter plasmid (5.4 Kbp) and luciferase plasmid (Luci, 6.3 Kbp) per capsid, these AVs transduced both the reporter plasmids into human embryonic kidney HEK293T(293) cells at near 100% efficiency.

FIG. 4 shows the Quantification of packaged GFP and luciferase DNAs for T4-AVs described in the present disclosure. As shown in FIG. 4, the linearized DNAs are incubated with T4 at increasing DNA-to-capsid ratios as indicated at the top of the panels, with the red arrows indicate the position of the packaged GFP (408) and luciferase DNA band(s) (410) as analyzed by agarose gel electrophoresis. The top panel of FIG. 4 (402) shows the agarose gel electrophoresis of the packaged GFP DNA band(s), the middle panel of FIG. 4 (404) shows the agarose gel electrophoresis of the packaged luciferase DNA band(s), the bottom panel of FIG. 4 (406) shows the agarose gel electrophoresis of both packaged GFP and luciferase DNA band(s). Maximum packaging capacity is reached at a ratio of 15-20:1.

FIG. 5 shows the efficient delivery of packaged DNA by T4(GFP)-AVs into 293 cells, at the MOI of 10³, 10⁴ and 10⁵. The T4(GFP)-AVs delivered is determined by GFP expression, as shown in the left column (502) of FIG. 5. Cell nuclei are stained and visualized with Hoechst, as shown in the middle column (504) of FIG. 5. The right column (506) of FIG. 5 shows the co-localization of T4(GFP)-AVs delivered and the cell nuclei, indicating the efficient delivery of T4(GFP)-AVs. Furthermore, the top row (508) of FIG. 5 shows the delivery of T4(GFP)-AVs at MOI of 10³. The middle row (510) of FIG. 5 shows the delivery of T4(GFP)-AVs at MOI of 10⁴. The bottom row (512) of FIG. 5 shows the delivery of T4(GFP)-AVs at MOI of 10⁵.

FIGS. 6 and 7 show the effect of T4 and lipid complexation volume and time on DNA delivery efficacy, determined by luciferase activity. The luciferase activity is measured by relative luminescence unit. As shown in FIG. 6, the relative luminescence unit is impacted by complexation volume and maximizes at the complexation volume of 100 μl. As shown in FIG. 7, the relative luminescence unit is also impacted by complexation time and maximizes at the complexation time of 10 min. FIG. 8 shows the transduction efficiencies of AVs coated with different cationic lipids, including LPF2K-AV (808), LPFRNAiMAX-AV (810), LPF3K-AV (812), LPFLTX-AV (814), LPFStem-AV (816), EXPI-AV (818) and FECT-AV (820), while the cell control (802), the “naked” T4 (Luci) capsid (804) and cationic T4 (Luci) capsid without lipid (T4 (Luci)-TAT) (806) are used for comparison.

Under optimal conditions (the complexation volume is 100 μl and the complexation time is 10 min), the luciferase activity of capsids with cationic lipid coat (808 through 820) is ˜10⁵-fold higher than the “naked” capsids (804) lacking the cationic lipid coat, and ˜10²-fold higher than the capsids that are cationic but lacked the lipid (806). The latter capsids (806) are prepared by displaying a cationic cell penetration peptide, HIV-TAT (NGYGRKKRRQRRRG)⁵⁵. As shown in FIG. 8, no major differences are observed with various cationic lipids, although LPF2K and LPFRNAiMAX gave the best transduction efficiencies. Relatively low amounts of lipids were sufficient to coat the capsids and no significant cell toxicity is observed. FIG. 9 shows the optimal ratio of T4 head particles to LPF2K concentration on delivery efficacy, as indicated by luminescence activity, and cell viability. Luminescence activity (histogram) and cell viability assay (blue line) are performed at 48 h post-transduction. Quantification of the number of viable cells in culture is based on the determination of ATP present, which signaled the presence of metabolically active cells, as determined by luminescent cell viability assay. Percent viability is calculated in comparison with the untreated control. As shown in FIG. 9, the delivery efficacy increases with the ratio of T4 head particles to LPF2K concentration, while the cell viability remains at about 100% at all ratio of T4 head particles to LPF2K concentration tested. FIG. 10 shows the optimization of the LPF2K amount for complexing with 2×10¹⁰ T4(Luci) (histogram) and relative cell viability (blue line). As shown in FIG. 10, the complexing increases with the LPF2K amount, while the cell viability remains at about 100% when the LPF2K amount is no greater than 2.5 μl, but decrease with increasing LPF2K amount, when the LPF2K amount is greater than 2.5 μl.

In one embodiment, AVs packaged with two therapeutically relevant expression plasmids, the heavy (H) and light (L) chain plasmids of VRC01 antibody, a potent broadly neutralizing antibody against HIV-1⁶⁴, are assembled. Thus, these AVs can co-deliver more than one plasmid. FIG. 11 shows the quantification of packaged VRC01 plasmid for T4-AVs at different DNA to T4 ratio, as analyzed by agarose gel electrophoresis. The linearized DNAs are incubated with T4 at increasing DNA-to-capsid ratios as indicated at the top of the panels. As shown in FIG. 11, the DNAs packed and analyzed are VRC01 heavy chain along, VRC01 light chain alone, VRC01 heavy and light chains as one molecule and VRC01 heavy and light chains as separate molecules but packed in one T4-Avs particle. Maximum packaging capacity is reached at a ratio of 15-20:1. Therefore, an average of 10-12 molecules of H and L plasmids are packaged per capsid. FIG. 12 shows the quantification of the amount of VRCO1 antibody secreted by transduced cells. A HIV gp120 envelope protein-specific ELISA is conducted to quantify the amount of VRCO1 antibody secreted by 293 cells 48 h following T4-AV transduction. The inset (1202) shows the packaging of VRCO1 heavy chain H (blue arrow), light chain L (red arrow), H+L chains, and H−L single chain (green arrow). As shown in FIG. 12, these VRC01-AVs efficiently co-transduce and co-express the H and L chains, as evident from the secretion of functional immunoglobulin (Ig) molecules at high levels (˜4.5 mg/liter). These levels are about 20-fold higher than when the H and L chains are delivered by cationic-only (TAT-displayed) AVs lacking the lipid coat. In FIG. 12, the amounts of VRCO1 antibody secreted by transduced cells infected by viral particles lacking the lipid coat are shown in columns labelled as “cell control”, “T4(HL)-HocTSocT” and “T4(H+L)-HocTSocT”, while those of cells transduced with AVs with the lipid coat are shown in columns labelled as “T4(HL)-AV”, “T4(HL)-SocT-AV”, “T4(H+L)-AV” and “T4(H+L)-SocT-AV”. Naked particles lacking either the cationic or the lipophilic character produced very low levels of the antibody.

In another embodiment, four plasmids containing two H and two L chains belonging to two different HIV-1 antibodies, VRC01 and CH58, are packed into the same capsid. FIG. 13 shows the quantification of packaged VRC01 and CH58 plasmids for T4-AVs at different DNA to T4 ratio, as analyzed by agarose gel electrophoresis. The linearized DNAs are incubated with T4 at increasing DNA-to-capsid ratios as indicated at the top of the panels. According to FIG. 13, an average of ˜11 molecules, mixture of four different plasmids, are packaged in the same capsid. FIG. 14 shows the quantification of the amount of VRCO1 and CH58 antibodies secreted by transduced cells. ELISA titers of secreted VRCO1 and CH58 antibody production by the 293 cells following AV(VRCO1+CH58) transduction are determined. These AVs when co-transduced into 293 cells secreted both the VRC01 (˜3 mg/liter) and CH58 (˜2 mg/liter) antibodies, according to FIG. 14.

The above sets of data demonstrate that the cationic lipid-coated T4-AVs efficiently co-deliver and co-express multiple recombinant plasmids in human cells, as well as assemble functional Ig complexes. The efficiency of AV delivery is remarkably high, considering that it is a phage-based platform. FIG. 15 shows a head-to-head comparison of transduction efficiencies of T4-AVs and AAVs as determined by luciferase activity at the ratio of 10³, 10⁴, and 10⁵ nanoparticles per cell. According to FIG. 15, the T4-AVs gave ˜10-40 fold greater expression of the luciferase reporter gene than that of AAV, one of the most efficient and widely used viral vectors for gene therapy³³. This might be because the T4-AVs can deliver multiple copies of a genetic payload in a single transduction event, whereas AAV and other vectors such as lentiviruses are limited to delivering only one copy at a time.

However, the mechanisms involved in entry, uncoating, and intracellular trafficking of T4-AVs are not completely understood. To understand the entry and intracellular trafficking pathways used by T4-AVs, cellular uptake of T4(Luci)-AVs is analyzed by treatment with various inhibitors. In one embodiment, cells are pretreated with various inhibitors for 30 min before exposure to T4(Luci)-AVs. FIG. 16 shows the comparison of luciferase expression with the presence of different compounds. Compounds such as sucrose and chlorpromazine, inhibitors of clathrin-mediated endocytosis, methyl-β-cyclodextrin (M-β-CD), a cholesterol-depleting agent, and dynasore, a dynamin-mediated endocytosis inhibitor, can cause profound reduction in AV delivery. Furthermore, the GFP expression with the presence of selective inhibitors is also compared, as shown in FIG. 17. the GFP expression reflects delivery efficacy. According to FIG. 17, the level of GFP expression with the presence of cytochalasin D is about the same as when do drug/inhibitor is added, while the presence of chlorpromazine, M-β-CD, sucrose, and dynasore reduces the level of GFP expression, which is consistent with the luciferase expression data shown in FIG. 16. This evidence suggests that the T4-AVs are internalized through dynamin- and clathrin-dependent endocytosis, in which plasma lipid raft also probably plays an important role¹². The lipid coat apparently facilitated the escape of T4-AVs from the late endosome into the cytosol where uncoating and release of cargos occurred. Chloroquine, a compound known to enhance the endosomal escape of cationic T4-TAT⁶⁵, does not further enhance the already very efficient delivery by the cationic lipid-coated T4-AVs. Furthermore, Tubastatin A (TBA), a microtubule-binding agent that stabilizes microtubules and facilitates transport of DNA from the cytosol to nucleus³ significantly can enhance the reporter signal of the AV-packaged DNA molecules. FIG. 18 shows the enhancement of reporter signal of the AV-packaged DNA molecules when the amount of TBA added is 4 μM (1806), 8 μM (1804) and 16 μM (1808), compared to when no TBA is added (1802).

Co-Delivery of Genes and Proteins by T4 Artificial Viruses

In one embodiment, T4-AVs can co-deliver proteins along with genes. A series of AVs are assembled by displaying proteins fused to either Soc or Hoc. FIG. 19 shows the locations of Soc-fused (1902) and Hoc-fused protein (1904) and DNA (1906) cargos carried by T4-AVs. A series of proteins having different size, charge, oligomeric state, and function are incorporated, which are summarized in the table below.

MW Protein Copies/ Displayed protein (KDa) charge Function capsid Cas9-Soc (SEQ ID 169.2 +25 RNA-guided- 550 NO: 16) DNA endonuclease Cpf1- Soc (SEQ ID 159.6 +13 450 NO: 17) Cre-Soc (SEQ ID 49.2 +11 DNA recombinase 630 NO: 22) Cre-Hoc (SEQ ID 80.9 +11 95 NO: 18) Soc-TAT 25.8 +8 Cell penetrating 750 RGD-Hoc (SEQ ID 45.5 −1 Cell adhesion motif 85 NO: 19) GFP-Soc 35.5 −8 Fluorescent protein 660 β-Gal-Soc 128.8 −40 Glycoside hydrolase 320 Soc-RGD 10.1 −1 Cell adhesion motif 710

In one embodiment, the display of Soc- and Hoc-fused proteins on T4 capsids is analyzed by gel electrophoresis.

FIGS. 20 and 21 show binding patterns at different ratios that indicate that saturation reached at ˜15-20:1 ratio, which is consistent with the previously reported data using many other proteins (not shown). FIG. 20 shows the position of β-Gal-Soc (2002) and the major capsid protein gp23* (2004), which is used as an internal control to determine the copy number of displayed β-Gal-Soc per capsid particle. FIG. 21 shows the position of Cre-Hoc (2102) and the major capsid protein gp23* (2104), which is used as an internal control to determine the copy number of displayed Cre-Hoc per capsid particle.

Soc-TAT, GFP-Soc, Cre-Soc (SEQ ID NO: 22), β-Gal-Soc, Cpf1-Soc, Cas9-Soc (SEQ ID NO: 16), RGD-Hoc, and Cre-Hoc are overexpressed, purified, and incubated with purified T4 heads at increasing ratios of protein molecules to Soc- or Hoc-binding sites. FIG. 22 shows the positions of various displayed proteins, including Soc-TAT (2210), GFP-Soc (2208), Cre-Soc (2206), β-Gal-Soc (2204), Cpf1-Soc (2212), Cas9-Soc (2214), RGD-Hoc (2218), and Cre-Hoc (2216), and the major capsid protein gp23* (2202), which is used as an internal control to determine the copy number of displayed protein per capsid particle.

In one embodiment, all the AVs in the present disclosure efficiently co-delivered the displayed proteins as well as the packaged plasmids in a functional state. For instance, when exposed to 293 cells, the GFP-displayed AVs show strong green fluorescence, initially at the cell surface (˜3 hr) and then throughout the cell (˜20 hr). When the same AVs are also packaged with mCherry reporter plasmid, the cells in addition began showing red fluorescence at 6 hr and continued to intensify up to 48 hr, due to the expression of the delivered mCherry gene. FIG. 23 shows the quantification of packaged mCherry reporter plasmid (2302) for T4-AVs and the quantification of packaged backbone of plasmid pAAV-mCherry (2304) at different DNA to T4 ratio. The linearized DNAs are incubated with T4 at increasing DNA-to-capsid ratios as indicated at the top of the panels. Maximum packaging capacity reached at a ratio of 15-20:1. FIG. 24 shows the fluorescence of internalized GFP protein (2402) and expression of mCherry (2406) DNA in cells following delivery by T4(mCherry)-Soc-GFP-AVs. A merged view (2404) of both GFP and mCherry as well as a bright field (BF) view (2404) are also shown in FIG. 24. FIG. FIG. 25 shows representative fluorescent images of cells at 3 h after treatment with Soc-GFP (2502), Soc-GFP+LPF2K (simple mixture) (2504), T4-Soc-GFP (2506), or T4-Soc-GFP-AVs (2508). The right panel (2510) shows the merged image of GFP signal and bright field (BF), suggesting the displayed GFP protein efficiently attached to the cell surface at 3 h after AV transduction. FIG. 26 shows mCherry DNA delivery using T4(mCherry)-AVs where only mCherry expression is observed. In FIG. 26, GFP expression (control) (2602), expression (2604), merged view of GFP and mCherry (2606) as well as BF view (2608) are shown.

In one embodiment, cells transduced with AVs displaying ˜516 kDa tetrameric β-galactosidase (β-Gal) and packaged with Luci or GFP reporter plasmids, exhibit both the β-galactosidase activity and luciferase/GFP activity in a dose-dependent manner, as shown in FIGS. 27 and 28. FIG. 27 shows β-galactosidase enzyme activity and GFP expression examined following delivery by T4(GFP)-Soc-β-Gal-AVs at increasing copy numbers of displayed Soc-β-galactosidase. As shown in FIG. 27, the β-galactosidase enzyme activity and GFP expression increase with the increasing ratio of copies of β-galactosidase protein or GFP plasmid to T4 capsid.

Somewhat unexpectedly, as shown in FIG. 28, AVs with displayed proteins, including Soc-TAT (2806), GFP-Soc (2808), Cre-Soc (2810), β-Gal-Soc (2812), Cpf1-Soc (2814) (SEQ ID NO: 17), Cas9-Soc (2816) (SEQ ID NO: 16), RGD-Hoc (2818) (SEQ ID NO: 19), and Cre-Hoc (2820) (SEQ ID NO: 18), in general show enhanced transduction efficiency, as measured by the luciferase activity, when compared to control AVs (2804) having no displayed protein probably because the displayed protein molecules contributed additional charges that result in better lipid coating and/or cell binding. Consistent with this notion, more positively charged proteins such as TAT (2806), Cas9 (2816), and Cpf1 (2814) show greater enhancement, with the TAT-AVs having high copy number (520 Copies) and high positive charge of TAT showing the highest enhancement, ˜3.5-fold. FIG. 29 shows representative fluorescence images depicting enhanced transduction of TAT-displayed T4-AVs at different copy numbers of TAT per capsid and at different ratios of T4-AV nanoparticles per cell. FIG. 30 shows Soc-TAT decoration increases the delivery efficiency of T4(GFP)-AVs into 293 cells. Soc-TAT molecules are displayed on T4(GFP) capsid at increasing ratios of Soc-TAT molecules to Soc binding sites (0:1to 20:1). As shown in FIG. 30, the delivery efficiency increases with the increasing ratios of Soc-TAT molecules to Soc binding sites. The resultant T4(GFP)-Soc-TAT-AVs are transduced into cells at a ratio of 10⁵ T4-AVs per cell. The GFP fluorescence is observed at 20 h post transduction.

The 9-aa disulphide-constrained RGD peptide (CDCRGDCFC) (2818 and 3104), a cell surface binding ligand, when fused to the tip of Hoc fiber showed even greater enhancement, compared to control AVs (T4(Luci)-AV) (2804 and 3102). The blue line (2802) in the top of FIG. 28 shows that cell viability of cells treated with T4-AV particles with various displayed proteins remains at about 100%.

This tripeptide motif (RGD peptide) has been well-documented to bind to the abundantly present integrin molecules on human cells⁸. Furthermore, the luciferase activity of the Hoc-fused RGD (RGD-Hoc-T4(Luci)-AV) (3104) is ˜5-fold higher than the Soc-fused RGD (RGD-Soc-T4(Luci)-AV) (3106), as shown in FIG. 31, even though the copy number of Soc-RGD is 8.3-fold greater than that of RGD-Hoc. It appears that the targeting ligand attached to the tip (N-terminus) of ˜17 nm-long flexible Hoc fiber imparts much greater reach to capture the integrin receptor molecules than the Soc-fused RGD that is bound to the capsid wall.

Genome Editing Artificial Viruses

Ability to “program” AVs with combinations of genes and proteins can be used to perform complex molecular operations in human cells, which would open a vast array of therapeutic applications^(7,62).

In one embodiment, a variety of genome editing AVs are assembled by incorporating all the editing molecules into the same AV in different configurations, summarized in the table below.

Payloads of genome editing T4-AVs Packaged inside Displayed outside 1 Cas9; gRNA; GFP — 2 gRNA; GFP Cas9 3 GFP Cas9-gRNA(RNP) 4 Cas9; gRNA; GFP Cas9-gRNA(RNP) 5 Cas9; gRNA1; gRNA2 RNP1; RNP2

In a preferred embodiment, AVs packaged with plasmids carrying expressible Cas9 and gRNA genes under the control of CMV and U6 promoters, respectively, are assembled. Cas9 sequence is codon-optimized and fused with the nuclear localization sequence (NLS) PKKKRKV at its N-terminus (NLS-Cas9). This allows the transport of cytosol-delivered Cas9 into the nucleus to carry out genome editing. The gRNA is targeted to the PPP1R12C locus on chromosome 19 of the human genome, also known as the AAVS1 safe harbor locus¹⁰. On average, each capsid is packaged with 7 molecules of the 8.3 Kbp plasmid containing both the expression cassettes.

In another embodiment, AVs are assembled by incorporating purified Cas9 as displayed protein fused to Soc (NLS-Cas9-Soc), while the gRNA is supplied as a packaged plasmid. The purified NLS-Cas9 (panel A of FIG. 32) and NLS-Cas9-Soc (panel B of FIG. 32) are obtained using size-exclusion chromatography and the purification of NLS-Cas9 and NLS-Cas9-Soc is confirmed by SDS-PAGE, as shown in FIG. 32.

FIG. 32 shows the expression cassette schematics and size-exclusion chromatography profiles of Cas9 and Cas9-Soc, respectively. Soc is fused to the C terminus of Cas9. Both Cas9 and Cas9-Soc contain an N-terminal SV40 nuclear localization signal (NLS) and a C-terminal His tag. The proteins are over-expressed in E. coli using the T7 promoter and purified by HisTrap affinity chromatography and size-exclusion chromatography. The purified Cas9 and Cas9-Soc exist as monomers, as evident from the molecular size determined using the respective elution volumes. The purified proteins are analyzed by SDS-PAGE as shown in the inserts.

Up to about 550 molecules of Cas9 could be displayed on the surface when the assembly mixture contains Cas9 (3302) at a ratio of 10 molecules to one Soc binding site, as shown in FIGS. 33, and ˜10 copies of gRNA plasmid (3402) are packaged inside the capsid, as shown in FIG. 34. FIG. 33 also shows the display of Cas9-Soc on T4 capsid at increasing ratios of Cas9-Soc molecules to Soc-binding sites. The positions of Cas9-Soc (3302) and gp23* (3304) bands on an SDS-gel are shown.

In another embodiment, a second GFP reporter plasmid is packaged into both these AVs to confirm that the AV transduction is at near 100% efficiency, a benchmark for all T4-AV studies in the present disclosure, as shown in FIG. 35. As shown in FIG. 35, fluorescence microscopy images show enhanced GFP reporter expression with increasing copy number of displayed Cas9.

Furthermore, a series of biochemical assays are performed to ensure that Cas9 and gRNAs exhibited full functionality, i.e., formation of Cas9-gRNA ribonucleoprotein (RNP) complexes and gRNA-directed cleavage of target DNA, as shown in FIGS. 36 and 37. The binding test of Cas9 and Cas9-Soc to AAVS1 gRNA1 or gRNA2, as determined by gel retardation assay. As shown in FIG. 37, Cas9 (3702 and 3706) and Cas9-Soc (3704 and 3708) showed comparable levels of DNA cleavage activity at the specific gRNA targeted sites. These AVs when transduced into 293 cells carry out genome editing by introducing double-stranded breaks at the targeted AAVS1 locus followed by repair by non-homologous end joining (NHEJ) which create short insertions and deletions (indels) at the target site, as determined by T7 Endonuclease I (T7EI) assay, as shown in FIG. 38, and confirmed by DNA sequencing (not shown). FIG. 38 shows the disruption of endogenous AAVS1 locus following AV-mediated delivery of Cas9 protein and gRNA-expressing plasmid DNA. Indel mutations are detected by the T7E1 assay three days after the transduction. FIG. 39 shows AAVS1 indel efficiency of T4-AVs displayed with various copy numbers of Cas9, including 50 copies (3902), 180 copies (3904), 280 copies (3906) and 460 copies (3908). The optimal efficiency of genome editing is ˜12 to 15%, when the Cas9 copies per T4 capsid is about 280 (3906).

In another embodiment, AVs are assembled by incorporating Cas9 (4002) and gRNA (4004) fused to Soc (4006) as a pre-formed ribonucleoprotein (RNP) complex, as shown in FIG. 40. Negative EM showed the presence of genome editing complexes decorating the Capsid (4102), as shown in FIG. 41. About 280 copies of ˜210 kDa Cas9-gRNA RNP complex are displayed on the capsid through Soc. As shown in FIG. 42, binding of gRNA (4204) to T4(GFP)-Soc-Cas9 capsids increases with increasing ratios of gRNA molecules to Soc binding sites, while the amount of GFP (4202) remains constant at all ratios. As shown in FIG. 43, binding of gRNA (4304) to T4(GFP)-Soc-Cas9 increases by increasing the ratio of Cas9-Soc molecules to Soc binding sites, while the amount of GFP (4302) remains constant at all ratios. FIG. 44 shows the binding of gRNA to T4(GFP)-Soc-Cas9 did not affect the display of Cas9-Soc on T4, as the relative Cas9-Soc display does not significantly (N.S.) change at all gRNA to T4(GFP)-Soc-Cas9 ratios.

In another embodiment, an additional ˜7 molecules of Cas9-gRNA expression plasmid are packaged into the same AV.

In the above embodiments, either GFP or Luci reporter plasmids are also packaged to confirm near 100% transduction efficiency. FIG. 45 shows comparison of luciferase activity in cells treated with T4(Luci)-AVs or T4(Luci)-Soc-Cas9-gRNA-AVs at increasing gRNA binding ratio (0:1 to 4:1). The luciferase activity of T4(Luci)-Soc-Cas9-gRNA-AVs delivery is normalized to T4(Luci)-AVs and presented as the fold change. As shown in FIG. 45, T4(Luci)-Soc-Cas9-gRNA-AVs enhanced transduction efficiency, compared to T4(Luci)-AVs. FIG. 46 shows representative fluorescence images of cells treated with T4(GFP)-Soc-Cas9-AVs and T4(GFP)-Soc-Cas9-gRNA-AVs, which both show high transduction efficiency.

In one embodiment, the AVs with soc-fused proteins give the best editing efficiencies, ˜30-35% disruption and indels at the AAVS1 locus, about twice that obtained by lipofectamine transfection, as shown in FIGS. 47 and 48. FIG. 47 shows genome editing at the AAVS1 locus by RNP-AVs delivered at different ratios of AV nanoparticles to cells, as determined using T7E1 assay. FIG. 48 shows comparison of AAVS1 indel efficiencies using T4-AVs in different configurations, including T4-AV (4802), T4(Cas9-gRNA)-AV (4804), T4(gRNA-GFP)-Cas9-AV (4806), T4(GFP)-Soc-RNP-AV (4808), T4(Cas9-gRNA)-Soc-RNP-AV (4810), and Cas9-gRNA plasmid +Lip (4812). Empty T4-AVs and lipofectamine transfection (Lip) of Cas9-gRNA-plasmid are used as negative and positive controls, respectively.

In one embodiment, genome editing is performed at a therapeutically important site, by targeting the AVs to hemoglobin beta gene (HBB) on chromosome 11 of the human genome. AVs assembled with Cas9-HBB gRNA RNP complexes performed ˜20-25% editing at this site, as shown in FIG. 49. In FIG. 49, T7E1 assay shows HBB gene disruption (4902) mediated by T4(GFP)-Soc-Cas9-HBBgRNA-AVs.

In another embodiment, simultaneous editing at more than one site on the human genome is achieved by displaying two gRNAs, one targeted to HBB and another to AAVS1, on the same AV, as shown in FIG. 50. These AVs also carried ˜7 molecules of Cas9 and HBB/AAVS1gRNA expression plasmids. As shown in FIG. 50, these multiplex AVs successfully performed genome editing of the respective target sites, ˜20% at the HBB site (5002) and ˜30% at the AAVS1 site (5004).

Gene Recombination Artificial Viruses

In one embodiment, the T4-AVs can perform genome editing as well as gene recombination, homologous or site-specific, in the same cell. Previously, it was reported that Cas9-generated DNA breaks facilitate homologous recombination near the cleaved site^(6,28). In a preferred embodiment, AVs are assembled by displaying AAVS1-targeted Cas9-gRNA RNP complexes (5102) on capsid and a donor plasmid containing promoter-less puromycin resistant gene (Puro) (5104) packaged inside, as shown in FIG. 51. AV-mediated genome editing and homologous recombination at the AAVS1 locus (5106) is designed by delivering Cas9-gRNA RNP complex (displayed) (5108) and donor puromycin plasmid DNA (packaged) (5110). The donor plasmid also had ˜800 bp homologous arms flanking the Cas9 cleavage site. FIG. 52 shows the quantification of packaged puromycin plasmid DNA (5202) for T4-AVs. Puromycin resistance will emerge if homologous recombination occurred following Cas9 cleavage, bringing the Puro gene under the control of an upstream AAVS1 promoter, as shown in FIG. 51. Indeed, puromycin resistance clones arise following transduction by these AVs, whereas control AVs lacking the RNP complex showed no puromycin resistance. PCR and DNA sequencing show that 15 out 15 isolated single cell clones exhibiting puromycin resistance contained Puro gene (5302) insertion precisely at the Cas9 cleavage site, as shown in FIGS. 53 and 54 (FIGS. S5A and S5B). In the PCR assay, primers corresponding to the flanking AAVS1 gene were used for PCR. Three representative clones are shown in FIG. 53, all depicting homozygous recombination at the target site. FIG. 55 shows the locations of PCR amplification primer sets (P1 and P2, P3 and P4) for detecting targeted insertions. The sequences of the primer sets are:

P1: (SEQ ID NO: 12) CTGCCGTCTCTCTCCTGAGT P2: (SEQ ID NO: 13) GTGGGCTTGTACTCGGTCAT P3: (SEQ ID NO: 14) AAAACTGACGCACGGAGGAA P4: (SEQ ID NO: 15) GTGGATTCGGGTCACCTCTC

In FIG. 55, SA is short for splice acceptor site; T2A is short for 2A cleavage peptide from Thosea asigna virus capsid protein. Using the primers schematic showed in FIG. 55, PCR assay of the AAVS1 gene is performed on the DNA isolated from single cell clones of T4(Puro-donor)-Soc-Cas9-gRNA-AVs treated cells. Ten representative single cell puromycin-resistant clones (I1 to I10) are analyzed using each primer set. The result of PCR assay is shown in FIG. 56, confirming the presence of the amplified sequences and, thus, the Puro gene.

In one embodiment, AVs programmed with an even more complex set of payload molecules are assembled. The capsids are displayed with the site-specific recombinase Cre (with NLS at N-terminus) as Hoc fusion protein, and a plasmid containing CMV promoter-LoxP-polyA STOP-LoxP cassette upstream of the GFP reporter gene (LSL-GFP) is packaged inside the capsid, as shown in FIG. 57. T7E1 assay (5702) shown in the box indicates efficient and simultaneous genome editing by Cas9-gRNA RNP complex at an independent target site. The 34-bp LoxP sequences provide recombination sites for Cre. Successful site-specific recombination occurring between the LoxP sites splices out the polyA transcriptional STOP sequence and bring the GFP reporter under the control of the upstream CMV promoter, as shown in FIG. 57. FIG. 58 is a schematic of Cre-Hoc expression cassette. Hoc is fused to the C-terminus of Cre with a hexa-His tag and over-expressed in E. coli under the control of the T7 promoter. FIG. 59 shows the size-exclusion chromatography profile of Cre-Hoc protein. The red arrows indicate the eluted Cre-Hoc tetramer and monomer. The hatched box inside shows the SDS-PAGE analysis of Cre-Hoc tetramer and monomer. Both tetramer and monomer are active for phage display and site-specific recombination. Cre-Hoc recombinase catalyzes site-specific recombination of LSL-GFP DNA substrate which contains two loxP sites. The band pattern in FIG. 60 is consistent with what has been reported³⁰.

In another embodiment, these AVs also carried the Cas9-gRNA RNP complexes displayed on the surface and mCherry reporter plasmid molecules packaged inside, as shown in FIG. 57. FIG. 61 show co-display of Cas9-Soc (5:1, Cas9-Soc molecules to Soc binding sites) and Cre-Hoc at increasing ratios of Cre-Hoc molecules, as determined by SDS-PAGE analysis. FIG. 62 shows the impact of Cre-Hoc binding on the binding of Cas9-gRNA RNP on the same capsid. As shown in FIG. 62, both Cas9-gRNA RNP and Cre-Hoc bound to the same capsid and increasing Cre-Hoc display did not affect Cas9-gRNA RNP binding.

FIG. 63 shows the quantification of packaged LSL-GFP plasmid DNA (6302) and mCherry reporter plasmid (6304) for T4-AVs described in the above two embodiments. The linearized DNAs are incubated with T4 at increasing DNA-to-capsid ratios as indicated at the top of the panels. Maximum packaging capacity reached at a ratio of 15-20:1.

Together, this constitutes a large payload; 50 molecules of Cre, 270 molecules of RNP complex, 6 molecules of GFP donor plasmid, and 5 molecules of mCherry reporter plasmid in the same AV. Remarkably, these AVs performed all the tasks they are programmed with. First, the RNPs carry out genome editing at the AAVS1 site to ˜30% editing efficiency. Second, strong green fluorescence is observed in nearly 100% of 293 cells demonstrating efficient site-specific recombination by Cre, whereas control AVs lacking Cre showed no significant fluorescence, as shown in FIG. 64. LSL-GFP and mCherry DNAs are co-delivered and co-expressed in each cell, with the GFP expression occurring following recombination by co-delivered Cre protein, all through the same AV. FIG. 65 shows representative GFP expression images following transduction of 293 cells with Cre-Hoc-T4(LSL-GFP)-Soc-Cas9-gRNA-AVs at increasing Cre-Hoc display ratio. As shown in FIG. 65, the GFP expression increases with increasing Cre-Hoc display ratio. Third, the intensity and distribution of green fluorescence are comparable to that of mCherry fluorescence generated from the direct expression of a reporter gene that requires no recombination, as shown in the lower row in FIG. 64. This means that Cre, after AV entry and disassembly get re-located to the nucleus by virtue of its nuclear localization signal and perform LoxP recombination on the co-delivered and independently re-located GFP donor plasmid in nearly 100% of cells, which then lead to efficient transcription of GFP reporter from the upstream CMV promoter.

The high efficiency of site-specific recombination by T4-AVs is also verified by another approach. A stable 293 cell line is constructed by integrating a LoxP-mCherry-LoxP-polyA-STOP cassette upstream of promoterless GFP reporter gene. Then, AVs programmed with Cre, Cas9-gRNA RNPs, and Luci reporter plasmid are delivered into these cells that result in several genome modifications. The steps of verification are illustrated in FIG. 66, which is a schematic of Cre-Hoc-T4(Luci)-Soc-Cas9-gRNA-AVs delivery into Cre reporter cells. First, efficient Cre-mediated site-specific recombination occur, as evident by the cells showing strong red fluorescence but no green fluorescence at the start due to endogenous mCherry expression, which then turn into intensely green fluorescent, while the red fluorescence fades. This means that the transcriptionally active mCherry gene is spliced out by intramolecular recombination between the flanking LoxP sites by the AV-delivered Cre, in turn activating GFP reporter expression which now come under the control of an upstream promoter, as shown in FIG. 67. Second, the AVs co-delivered the Luci reporter gene which is expressed at high efficiency at all Cre-Hoc to T4(Luci)-Soc-Cas9-gRNA ratios, as shown in the left panel of FIG. 68. Third, these AVs also carried out efficient genome editing at another targeted site on the human genome, as evident from ˜30% gene disruption at the AAVS1 locus, as shown in the left panel of FIG. 68.

RNA Delivering Artificial Viruses

In another embodiment, this system is adapted for general RNA delivery including siRNAs, in light of strong interaction observed between Cas9 and gRNA and efficient delivery of the resultant RNP complexes by T4-AVs, as described in the above embodiments. siRNAs are ˜20-25 bp double-stranded oligonucleotides that target mRNA(s) having the same sequence for degradation instead of translation. Such siRNA-mediated gene silencing mechanism has been extensively used for treatment of various genetic and infectious diseases¹³.

Cas9 efficiently binds to siRNA. In vitro gel retardation experiments show that gRNA can replace bound siRNA in the Cas9-siRNA complex. FIG. 69 shows the result of an electrophoretic mobility shift assay, determining the gRNA/siRNA:Cas9-Soc binding stoichiometry. In the electrophoretic mobility shift assay, a constant amount of gRNA or siRNA is mixed with various molar ratios (0:1 to 5:1) of Cas9-Soc molecules for 1 hat room temperature and then analyzed by agarose gel electrophoresis. The gRNA/siRNA-Cas9-Soc complexes remained in the loading well. With the increasing ratios of Cas9-Soc to gRNA/siRNA, the amount of gRNA/siRNA-Cas9-Soc complexes remained in the loading well increases.

In one embodiment, the T4-AVs are decorated with Cas9-siRNA RNP and/or Cas9-mRNA RNP complexes. In a preferred embodiment, the T4-AVs are decorated with ˜280 Cas9-siRNA RNP complexes. The configurations of T4-AVs carrying siRNA and mRNA payloads are summarized in the table below. FIG. 70 is a schematic of T4-AVs carrying siRNA and mRNA payloads, with DNA (7002) packaged in T4 and RNP complexes, containing Cas9 (7004), mRNA (7006) or siRNA (7008) and Soc (7010), displayed outside. The binding of siRNA to the T4(gRNA-GFP)-Soc-Cas9 capsids increases with the increasing ratios of siRNA molecules to Soc binding sites, as shown in FIG. 71.

Payloads of RNA T4-AVs Packaged inside Displayed outside gRNA; GFP/Luci Cas9-siRNA1 gRNA; GFP/Luci Cas9-siRNA1&2 gRNA; mCherry/Luci Cas9-mRNA

In one embodiment, when exposed to 293 cells, these AVs, which also contain the packaged GFP or Luci reporter plasmids, efficiently delivered siRNA molecules and silenced GFP expression, while the control AVs delivering a nonspecific control siRNA (NCsiRNA) had no effect, as shown in FIG. 73. FIG. 72 shows that the siRNA:T4(Luci)-Soc-Cas9 ratios have no effect on the AV delivery efficiency. Luciferase expression of T4(Luci)-Soc-Cas9-siRNA-AVs delivery is compared to control transduction with T4(Luci)-Soc-Cas9-AVs (lacking siRNA) and presented as the fold change. In FIG. 74, western blotting quantification shows suppression of GFP protein levels by GFPsiRNA-AVs at 48 and 72 h post-transduction. Remarkably, up to ˜90% silencing is achieved in 48 hrs and near 100% silencing in 72 hrs by the T4-AVs, as shown in FIG. 74. The GFP suppression percentage is quantified in FIG. 75, which shows the GFP suppression percentage increases with the increase ration of siRNA to T4(GFP)-Soc-Cas9. Also shown in FIG. 75, the GFP suppression percentage reaches close to 100% at the ration of siRNA to T4(GFP)-Soc-Cas9 of 3:1.

In one embodiment, two siRNAs silencing different mRNAs could be simultaneously delivered. In a preferred embodiment, one of the two siRNAs into the same AV target to GFP gene and the other to the housekeeping gene GAPDH. AVs carrying GFP-siRNA and GAPDH-siRNA knock down the expression of both these genes by ˜95% and 80%, respectively, as shown in FIG. 76.

Delivery of much longer mRNA molecules would further expand the footprint of RNA-AVs to high-level expression of genes for therapeutic applications⁴⁶. In one embodiment, the siRNA of the above AVs is replaced with mRNA by simply mixing the in vitro transcribed 996-nt GFP mRNA with Cas9-T4 capsids. The Cas9-mRNA complexes are formed efficiently, reaching saturation at ˜8:1 ratio of mRNA to Cas9 molecules, as shown in FIG. 77, while no significant mRNA binding is evident with the control capsids lacking Cas9. FIG. 77 shows the loading of GFPmRNA on T4(mCherry)-Soc-Cas9 capsids at increasing ratios of mRNA molecules to Soc binding sites, which remains the same after the ratios of mRNA molecules to Soc binding sites reaches 8:1. This result is confirmed by an electrophoretic mobility shift assay showing the binding of mRNA to Cas9-Soc protein at increasing ratios of Cas9-Soc molecules to mRNA (0:1 to 7:1), as shown in FIG. 78. Each AV carried a payload of ˜55 molecules of mRNA. The lower copy number of mRNA when compared to siRNA is probably because the much longer mRNA titrated several molecules of Cas9.

In one embodiment, the GFPmRNA-AVs described in the above embodiment upon transduction into 293 cells express strong green fluorescence in the cells, and the fluorescence is evenly distributed throughout the cell and merges with the red fluorescence generated by co-delivery of mCherry reporter gene packaged in the same AV, as shown in FIG. 79. On the other hand, control (mCherry)AVs lacking the Cas9-mRNA complex showed only red fluorescence, as shown in FIG. 80. Additionally, expression of packaged Luci reporter suggested that mRNA display does not affect the AVs' efficient transduction, as shown in FIG. 81. Luciferase expression is compared with the control AVs lacking mRNA display and presented as the fold change.

In another embodiment, another gRNA expression plasmid is packaged into the above AVs, to further enhance the utility of the RNA-AVs. FIG. 82 shows the quantification of packaged gRNA expression plasmid (AAVS1 gRNA) (8202). With this configuration, upon delivery, the displayed Cas9 can first deliver siRNA or mRNA into the cytosol and then, by virtue of the fused NLS sequence, it can re-locate to the nucleus and form a genome editing complex with the gRNA expressed from the co-delivered plasmid. Cas9 then can perform a second function, genome editing at the target site.

Control in vitro experiments show that gRNA can replace bound siRNA in the Cas9-siRNA complex as shown in the left panel of FIG. 83, whereas the reverse, siRNA replacement of gRNA in the Cas9-gRNA complex, does not occur, as shown in the right panel of FIG. 83. In one embodiment, the AVs are programmed with displayed Cas9-siRNA or Cas9-mRNA complexes and packaged inside the gRNA and mCherry reporter plasmids, by taking advantage of these differential affinities of Cas9 to siRNA and gRNA. In one embodiment, upon transduction into 293 cells, these AVs perform GFP gene silencing or GFP mRNA expression, genome editing at AAVS1, and mCherry expression in the same cell, as shown in FIGS. 84 and 85. FIG. 84 shows Quantification of AAVS1 indel frequencies of cells treated with T4(AAVS1gRNA-GFP)-Soc-Cas9-siRNA-AVs at increasing ratios of siRNA molecules to soc binding sites. The box on the right shows AAVS1 gene disruption using the T7E1 assay. FIG. 85 shows the quantification of genome editing at AAVS1 locus by T4(AAVS1gRNA-mCherry)-Soc-Cas9-GFPmRNA-AVs at increasing ratios of mRNA molecules to capsid-displayed Cas9.

Maximizing the Programmability of T4 Artificial Viruses

A CRISPR strategy⁵³ that allows filling of the interior capsid space with proteins in addition to DNAs has been developed, to further amplify the programmability of T4-AVs. This would not only increase the cargo capacity but also impart a novel property to T4-AVs, ability to assemble DNA-protein complexes in situ within the nano-capsid compartment that could, after delivery, guide the transport of DNA cargo to the nucleus. Such a guided transport system (GTS) could be adapted in future for guiding the cargos to appropriate intracellular destinations.

During phage T4 morphogenesis⁶⁷ the major capsid protein gp23 assembles around a scaffolding core formed by a cluster of proteins including three nonessential histone-like “internal proteins”; IPI, IPII, and IPIII. Following assembly, most of the scaffold proteins are degraded to small peptides, which then leave the capsid creating space for genome encapsidation. The IPs, however, are cleaved only once, next to a ˜10 amino acid N-terminal capsid targeting sequence (CTS). While the CTS leaves the capsid, the highly basic IPs, ˜1,000 molecules in total, remain inside the capsid and protect the genome after the DNA-protein complex is injected into the host E. coli during phage infection. Previous studies showed that when the C-terminal portion of the IPs is replaced with foreign proteins, the N-terminal CTS targets the foreign proteins to the core, which after CTS removal remain in the capsid space³².

In one embodiment, a CRISPR strategy is developed, by which Lad repressor protein molecules are packaged inside the capsid, which can then form complexes with the packaged DNA containing an engineered lac operator sequence (LacO) in trans. An “acceptor” phage is first generated by deleting ipI and ipII genes and this phage is used to infect E. coli containing two plasmids; a spacer plasmid that expresses Cas9 or Cpf1 and CRISPR RNA corresponding to a protospacer sequence in the deleted region of the acceptor phage, and a second donor plasmid containing the Lad repressor gene fused to CTS sequence at the N-terminus and NLS sequence at the C-terminus (CTS-LacI-NLS or CLN) (SEQ ID NO: 20) flanked by ˜200 bp homologous arms (FIG. S7A). FIG. 86 is a schematic depicting the programmable guided transport system (GIS) using CRISPR-engineered T4-AVs: a. engineering of CTS-LacI-NLS (CLN) mutant phage by CRISPR genome editing. b. preparation of CLN-packaged T4 heads in E. coli. c. CLN-packaged T4 head. d. CLN-DNA complexes formed in the CLN head following in vitro DNA packaging. e. GIS-T4 with Soc- and/or Hoc-displayed proteins. f. following delivery, the CLN-DNA complexes are guided to the nucleus by the NLS signal. Cleavage within the protospacer sequence of the acceptor phage genome by Cas9/Cpf1 editing complex followed by recombination between the cleaved ends and the homologous arms of donor plasmid transfer the CLN gene into phage genome by replacing the ipIII gene of the acceptor phage, as shown in FIG. 87. Panel A of FIG. 87 is a schematic of CRISPR-mediated CLN gene insertion (ipIII replacement); panel B of of FIG. 87 shows ipII gene deletion; and panel C of of FIG. 87 shows ipI gene (partial) deletion. The rescued recombinant phage thus is devoid of all three IPs but contained the CLN gene in their place. Empty capsids prepared from this CLN mutant phage (10 am.13 am.hoc⁻.soc⁻.CLN) contained ˜370 molecules of CLN protein inside the shell and show comparable in vitro DNA packaging efficiencies as the wild-type capsids. Successive rounds of CRISPR-mediated T4 genome editing to create the mutant phages is confirmed by PCR, as shown in FIG. 88. Size-exclusion chromatography profile of T4(CLN) heads is shown in FIG. 89. The arrow indicates the peak fraction of the packaging-competent T4(CLN) heads. The boiled and un-boiled T4 samples on SDS-PAGE demonstrate that the CLN-packaged T4 heads are expanded and behave similarly as the WT (wildtype) T4 heads. The head-packaged CLN protein is confirmed by SDS-PAGE (panel a of FIG. 90) and Western blotting (panel b of FIG. 90) and quantify its copy number. (E) Results of functional characterizations of CLN protein and T4(CLN) heads is shown in FIG. 91. Panel a of FIG. 91 shows the binding of CLN protein to LacO-containing plasmid DNA used for in vitro DNA packaging; in vitro DNA packaging in panel b of FIG. 91 shows that the mutant CLN heads exhibit comparable activity as the WT heads.

In one embodiment, the LacO sequence is inserted into the Luci or Cas9-gRNA plasmid and packaged into the CLN capsids. The packaged Lad repressor and LacO-DNA then form DNA-protein complexes as seen in in-vitro gel retardation experiments, as shown in FIG. 91. These AVs upon transduction into human cells showed enhanced expression of luciferase up to ˜3.5 fold, as shown in FIG. 92 and Cas9-mediated genome editing by ˜2 fold at the MOI of 10⁴, as shown in FIG. 93, presumably through enhanced transport of DNA-LacI complex to the nucleus due to the presence of NLS signal in LacI repressor. Panel a of FIG. 93 shows T7E1 assay result, while panel b of FIG. 93 shows frequency of AAVS1 indels, suggesting that T4(CLN)-GIS-AVs enhance genome editing. The luciferase or gene disruption enhancement is most significant, when the ratio of T4 particles to 293 cells is low, ˜10³:1 or ˜10⁴:1, but not at a high ˜10⁵:1 ratio. This is probably because the delivery of more copies of DNA at a high ratio compensated for the enhanced CLN-mediated transport at low copy numbers.

In one embodiment, genes for Cre recombinase are inserted into phage genome using the same strategy. In another embodiment, reporter genes for GFP and β-galactosidase packaging, which could be generally useful for viral genome engineering, are inserted. All these proteins are successfully packaged into T4 capsids, although the copy number varied.

Variations in size and structure of protein might affect their incorporation into the scaffolding core. FIG. 94 shows the biochemical characterization of GFP-packaged AVs. GFP protein packaging is confirmed by SDS-PAGE (panel a of FIGS. 94) and 488 nm excitation (panel b of FIG. 94). FIG. 95 shows the biochemical characterization of Cre-packaged AVs. Cre-heads is confirmed by SDS-PAGE (panel a of FIG. 95). However, all the packaged proteins retain their biological function; for instance, the packaged β-galactosidase oligomerize into functional tetramers and produce “blue phage” by exhibiting the glucoside hydrolase activity, as shown in FIG. 96. The left panel of FIG. 96 shows a size-exclusion chromatography profile of T4(β-gal) head. The arrow points to the peak fractions of eluted expanded T4(β-gal) capsids. In the right panel, the observation of “Blue phage” shows successful packaging of functional tetrameric β-galactosidase enzyme molecules and appearance of the blue color of the cleaved X-Gal substrate. Similarly, AVs packaged with GFP protein and mCherry plasmid DNA exhibit both green and red fluorescence, the former from delivered protein (“green fluorescence phage”) and the latter from delivered DNA, as shown in panel c of FIG. 94. The successful delivery of protein by green fluorescence phage is also confirmed by size-exclusion chromatography profile of T4(GFP) capsid, as shown in FIG. 97, and fluorescence images (FIG. 98) of T4(GFP) and control T4 capsids at 488 nm excitation showing the successful packaging of functional GFP in T4(GFP) capsids. The arrow in FIG. 97 points to the peak fractions of eluted expanded T4(GFP) capsids. Finally, AVs containing packaged Cre recombinase carry out efficient recombination between the LoxP sites of LoxP-mCherry-LoxP-polyA-STOP-GFP cassette to near 100% efficiency resulting in splicing out of the mCherry gene, which in turn allow expression of the GFP gene from an upstream promoter of the spliced product, as shown in panel b of FIG. 95. Therefore, the GTS strategy could be generally applied to DNA binding proteins that could carry out other genome modifications.

Ability to assemble artificial viruses that can be directed to perform defined molecular operations in human cells remained as the holy grail of medicine^(20,29,48). The present disclosure describes the proof of such a concept. A sequential assembly-line approach to build artificial viruses in the test tube is described, using the purified and well-characterized structural components of bacteriophage T4, each engineered to perform a specific task(s) in a human cell. These include: binding and entry into cells, intracellular trafficking, nuclear localization, and genome remodeling^(2, 37). In addition to creating enormous engineering space, this assembly-line approach allows mixing and matching of the components in desired combinations to generate varieties of artificial viruses endowed with specific therapeutic capabilities. Such a custom-buildable, “plug-and-play” artificial virus platform does not exist today, and several features distinguish it from other viral or synthetic delivery platforms currently available.

One of the features of the T4-AV platform is its ability to incorporate many types of therapeutic biomolecules including proteins, DNAs, RNAs, and their complexes in different compartments of the nanoparticle structure. These molecules, upon delivery into a human cell, faithfully execute their function(s) either independently or through interactions with each other. This has been demonstrated across a wide spectrum of molecules; proteins ranging from 27 kDa GFP to 516 kDa tetrameric β-galactosidase enzyme, nucleic acids ranging from large double-stranded plasmid DNAs to small single-stranded gRNAs, and preformed complexes including protein-protein, RNA-protein, and DNA-protein complexes in the present disclosure. Furthermore, analogous to natural viruses, functional circuits formed between delivered molecules upon AV “infection” that can also be tunable by adjusting the copy numbers of the cargo molecules, providing numerous options to create AVs with therapeutic capability.

The T4-AVs consistently generated signal to near 100% efficiency in the model cell line HEK293, as measured either by the expression of a reporter gene (e.g., Luci, GFP, mCherry) or by the activity of a delivered protein (e.g., GFP, β-Gal, Cre). A critical component of the AVs that contributed to high efficiency is the lipid coat, which is created by taking advantage of the highly anionic character of the T4 capsid. Off-the-shelf cationic lipids spontaneously bound to T4 capsid generating a lipophilic and cationic surface that is complementary to the anionic surface of human cells19, 23, 58, 66. Without this coat, the transduction efficiency is poor, as proven by the above embodiments. Even the AVs that are cationic but lacking the lipid coat showed a 100-fold lower signal. Furthermore, the lipid coat does not impair the display of Soc- and Hoc-fused protein molecules. On the other hand, these molecules, particularly the positively charged ones, further accentuate the T4-AV transduction efficiency.

The T4 artificial viruses described in the present disclosure breaks through four major barriers that currently exist for the delivery of biomolecules into human cells. First, the T4-AVs, unlike other delivery platforms, can efficiently deliver multiple copies of multiple and relatively large DNA molecules into cells in a single transduction event. This has been amply demonstrated using a series of plasmids containing reporter genes, antibody genes, and genome editing genes. This is possible not only because of the large cargo capacity of T4 but also because of the promiscuous nature of T4's packaging machinery that exhibits no sequence dependence^(43, 50, 56, 63). Consequently, the reporter signal as measured by luciferase activity is one of the highest reported, even higher than AAV transduction which can deliver only one reporter molecule per transduction event.

The second barrier that the T4-AVs breaks through is the all-in-one delivery. As demonstrated throughout our studies, the T4-AVs efficiently deliver complex cargos consisting of combinations of DNAs, proteins, RNAs, and their complexes. This is essential for many genome remodeling applications including genome editing and gene recombination that require co-delivery of multiple biomolecules, which is either currently not possible, or very difficult, with other delivery platforms^(36, 62). For example, for genome editing, AVs in different all-in-one configurations are assembled, carrying Cas9 nuclease and gRNAs either as functional RNA-protein complexes displayed outside and/or as expressible genes packaged inside. Similarly, for gene recombination, a variety of AVs are assembled that co-deliver the site-specific recombinase Cre and the donor plasmid.

The third barrier that the T4-AVs breaks through is multiplex delivery. T4-AVs are assembled by incorporating cargo molecules not only to target multiple sites (e.g., multiple gRNAs and siRNAs) but also to perform different molecular operations in the human genome. In one combination, three different operations; genome editing, gene expression, and site-specific recombination are performed by incorporating Cas9 and gRNA as RNPs, GFP or Luci genes as packaged plasmids, and Cre recombinase and donor plasmid as displayed and packaged molecules, respectively. In another combination, gene silencing, gene expression, and genome editing are performed by incorporating siRNAs, mRNA, Cas9, and gRNAs into the same artificial virus.

The fourth barrier that the T4-AVs breaks through is programmability, ability to carry out a set of instructions and also modify function upon entry into human cells. Many examples cited above demonstrate the execution of a set of instructions that each AV is programmed with. Modification of the functional behavior upon entry has also been demonstrated by the repurposing of Cas9 function. By taking advantage of the in vitro observation that Cas9 can bind to both single-stranded gRNA and double-stranded siRNA, and that the gRNA can dislodge bound siRNA due to its higher affinity for Cas9, AVs are assembled by displaying Cas9-siRNA complex and packaging gRNA expression plasmid. Upon entry, these AVs deliver siRNA into the cytosol that result in gene silencing while the same Cas9 then switch function to genome editing in the nucleus by binding to gRNA expressed from the co-delivered plasmid.

The programmability of T4-AVs is further enhanced by CRISPR engineering, which allow the incorporation of hundreds of protein molecules inside the phage capsid^(32, 53). Importantly, this created another avenue to generate additional functional circuits inside the packaged head that would lend itself to guiding intracellular trafficking and/or more effective genome modifications. These have been demonstrated using model proteins such as LacI and Cre. By pre-packaging LacI protein inside the capsid, it allows the formation of DNA-protein complexes between LacI protein and LacO-containing DNA arriving into the capsid in trans through in vitro DNA packaging. Once delivered, the engineered LacI with its nuclear localization signal then guide the DNA to nucleus as evident from enhanced reporter gene expression. Similarly, capsid-packaged NLS-Cre recombinase leads to near 100% efficiency of site-specific recombination in the human genome.

In conclusion, a new category of viral nanomaterial, phage-based artificial viruses, that can be custom-assembled in the test tube using an assembly-line approach is created. These artificial viruses possess similar architecture as natural viruses and go through similar pathways for entry, disassembly, and intracellular trafficking, although the exact mechanisms are not known and require further investigation^(37, 48). Importantly, however, from technology perspective, virtually unlimited varieties of AVs can be assembled using this approach that can faithfully execute functions each is programmed with and make precise alterations in genome and cellular metabolism. The systematic studies described in the present disclosure thus provide the necessary foundation to optimize payloads and create artificial viruses for efficient delivery into primary human cells that would lend itself for ex vivo cellular therapies such as stem cell and CAR T-cell therapies as well as in vivo therapies. These studies are in progress. With features such as large cargo capacity, ability to incorporate diverse cargos, programmability, customizability, and all-in-one delivery, this T4-AV platform established a powerful proof of concept for potential future applications to restore the health of defective human cells and ultimately the human body.

Having described the many embodiments of the present disclosure in detail, it will be apparent that modifications and variations are possible without departing from the scope of the invention defined in the appended claims. Furthermore, it should be appreciated that all examples in the present disclosure, while illustrating many embodiments of the invention, are provided as non-limiting examples and are, therefore, not to be taken as limiting the various aspects so illustrated.

EXAMPLES Example 1 Recombinant Protein Expression and Purification

Recombinant proteins (with the exception of Cas9 and Cpf1) were expressed by transforming the pET28b expressing plasmid in Escherichia coli (E. coli) BL21 (DE3) RIPL cells by the heat-shock method. The transformed cells were grown to an OD600 of 0.5 at 37° C. in Moores medium (20 g of tryptone, 15 g of yeast extract, 8 g of NaCl, 2 g of dextrose, 2 g of Na₂HPO₄, and 1 g of KH₂PO₄ dissolved in 1 L of Milli-Q® water) containing 50 μg/ml kanamycin and 25 μg/ml chloramphenicol, and protein expression was induced by 1 mM isopropyl β-d-1-thiogalactopyranoside (IPTG) at 30° C. for 3 h. After induction, cells were harvested by centrifugation, and the pellets are suspended in binding buffer (50 mM Tris-HCl, 300 mM NaCl and 20 mM imidazole, pH 8.0) containing proteinase inhibitor cocktail (Roche®, USA) and benzonase nuclease (Millipore Sigma®). The cell suspension was lysed by French press (Aminco®), and the soluble fraction was isolated from cellular debris by centrifugation at 34,000×g for 30 min. The lysate was filtered through 0.22-micron filters (Millipore®, Stericup®) and applied to a pre-equilibrated (binding buffer) HisTrapHP column (AKTA-Prime®, GE® Healthcare) and washed with binding buffer. The His-tagged protein was then eluted with a 20-500 mM linear imidazole gradient. The peak fractions were further purified by size exclusion chromatography using the Hi-Load 16/60 Superdex-200 (prep-grade) gel filtration column (GE® Healthcare) in GF buffer (20 mM Tris-HCl and 100 mM NaCl, pH 8.0) according to the manufacturer's instructions. The fractions containing the desired protein were pooled and concentrated by AmiconUltra-4 centrifugal filtration (10 kDa cut-off; Millipore®), flash-frozen in liquid nitrogen and stored at −80° C. All the column operations are performed at 4° C. Gel filtration molecular size standards were chromatographed on the same column to calculate the approximate size of the purified protein.

For Cas9-Soc or Cpf1-Soc purification, the recombinant SpCas9 or LbCpf1 used in this study was fused to Soc at the C-terminus and to nuclear localization signal peptide at the N-terminus. The protein also has a C-terminal hexa-histidine tag. Briefly, RIPL cells were cultured at 37° C. until OD600=0.6 and incubated at 20° C. for 40 min, then induced with 1 mM IPTG. After 20 h, the cells were collected and resuspended in 50 ml of binding buffer (50 mM Tris-HCl, 300 mM NaCl, 20 mM imidazole, and 5 mM Tris (2-carboxyethyl) phosphine (TCEP; Soltec Ventures), pH 8.0) containing proteinase inhibitor cocktail (Roche®, USA) and benzonase nuclease (Millipore Sigma®). The Cas9-Soc or Cpf1-Soc proteins were then purified by HisTrapHP and Superdex-200 columns as described above.

Example 2 T4 CRISPR Engineering

T4 phage engineering was performed according to a previously described procedure⁵³ . E. coli strains P301 (sup⁰) and B40 (sup¹) were used in the experiments described below. The 10-amber 13-amber hoc-del soc-del T4 phage was propagated on E. coli B40 as described previously⁶³. CRISPR-Cas9 or Cpf1 plasmids with specific spacer(s) were constructed by cloning spacer sequences into the streptomycin-resistant plasmid DS-SPCas (Addgene® No. 48645) (SEQ ID No. 21). The spacer sequences are shown below:

AAVS1-Cas9-gRNA1: (SEQ ID NO: 2) GTCCCCTCCACCCCACAGTG AAVS1-Cas9-gRNA2: (SEQ ID NO: 3) GGGGCCACTAGGGACAGGAT HBB-Cas9-gRNA: (SEQ ID NO: 4) AGTCTGCCGTTACTGCCCTG ipIII-Cas9-gRNA: (SEQ ID NO: 5) GGCCTTTACTACAGAAGCTT ipI-Cpf1-gRNA1: (SEQ ID NO: 6) TTCAGCAGGAGAGATAACGATTG ipI-Cpf1-gRNA2: (SEQ ID NO: 7) TACCATTACCGAAGCTACTCTTA ipII-Cpf1-gRNA1: (SEQ ID NO: 8) CTTCTAAGTTCGGCATGTCTATG ipII-Cpf1-gRNA2: (SEQ ID NO: 9) TTACGGTCTTTATCGGGCAA ipIII-Cpf1-gRNA1: (SEQ ID NO: 10) AAGTCGGAAGCCTTTGTAGCTAA ipIII-Cpf1-gRNA2: (SEQ ID NO: 11) TGCTTGGCAAATTCAAGACCTGC

The homologous donor plasmids were constructed by cloning the donor DNA into the pET28b vector. The CRISPR-Cas9/Cpf1 and donor plasmids are co-transformed into a suppressor containing E. coli B40 (sup¹), and then the positive clones are selected by streptomycin and kanamycin antibiotics. The cells transformed with either the CRISPR plasmid or the donor plasmid are used as controls. The cells were infected with WT or 10-amber 13-amber hoc-del soc-del T4 phages. The engineered genome of the progeny plaques was amplified and sequenced to confirm the insertion or deletion.

Example 3 T4 Heads Purification

The 10-amber 13-amber hoc-del soc-del T4 heads or protein-packaged GIS-T4 were isolated according to previously described protocols⁶³. Briefly, E. coli P301 (sup-) cells infected with mutant phages (500 ml of culture) were lysed in 40 ml of Pi-Mg buffer (26 mM Na₂HPO₄, 68 mM NaCl, 22 mM KH₂PO₄, and 1 mM MgSO₄, pH 7.5) supplemented with 10 μg/ml DNase I and 1 ml of chloroform, followed by incubation at 37° C. for 30 min to digest the DNA. After two rounds of low-speed (6,000×g for 10 min) and high-speed (35,000×g for 45 min) centrifugation, the pellet is resuspended in 200 μl of Tris·Mg buffer (10 mM Tris-HCl, 50 mM NaCl, and 5 mM MgCl₂, pH 7.5), followed by CsCl density gradient centrifugation. The extracted T4 heads were dialyzed overnight against Tris·Mg buffer and further purified by DEAE-Sepharose chromatography. The peak capsid fractions were concentrated and stored at −80° C. The number of particles were determined by quantification of the major capsid protein gp23* in comparison with the known amounts of phage T4, using SDS-PAGE and laser densitometry.

Example 4 DNA Packaging Assays

In vitro DNA packaging assays were performed according to a previously described procedure²⁴. The purified full-length gp17 (˜3 μM), the linearized DNA in packaging buffer (30 mM Tris-HCl, 100 mM NaCl, 3 mM MgCl₂, and 1 mM ATP, pH 7.5), and the purified T4 heads (˜2×10¹⁰ particles) were sequentially added to constitute a 20 ∞l reaction mixture. The mixture was incubated at 37° C. for 45 min, followed by the addition of benzonase nuclease and incubation at 37° C. for 30 min to remove excess unpackaged DNA. The packaged nuclease-resistant DNAs were released by treatment with 0.5 μg/μl proteinase K (Fermentas®), 50 mM ethylenediaminetetraacetic acid (EDTA), and 0.2% SDS for 30 min at 65° C. The packaged DNA was analyzed using 1% (wt/vol) agarose gel electrophoresis. The amount of packaged DNA was quantified by Quantity One software (Bio-Rad®). The packaging efficiency was defined as the average number of DNA molecules packaged in one T4 head.

Example 5 Protein and RNA Display on the T4 Head

Protein display on the T4 head is performed according to the basic protocols described previously²⁷. Briefly, after packaging linearized DNA as above, Soc- and/or Hoc-fusion proteins were added to the packaging mixture at different ratios and incubated at 4° C. for 1 h. The mixtures were sedimented by centrifugation at 30,000×g for 1 h, and unbound proteins in the supernatants were removed. After washing twice with PBS, the pellets were resuspended in PBS for SDS-PAGE analysis or Opti-MEM for cell transduction. After Coomassie Blue R250 (Bio-Rad®) staining and destaining, the protein bands on SDS-PAGE gels were quantified by laser densitometry (PDSI, GE® Healthcare). The densities of Hoc, Soc, and gp23* bands in each lane were quantified independently, and the copy numbers of bound Hoc or Soc fusion molecules per T4 were calculated using gp23* band in each lane as the internal control (930 copies per T4 capsid). For gRNA/siRNA/mRNA display, T4 heads displayed with Hoc or Soc fusion protein molecules was resuspended in RNAase-free PBS buffer, and then incubated with RNA at 4° C. for 1 h. The T4-RNP complexes were sedimented by centrifugation at 30,000×g for 1 h, and unbound RNAs in the supernatants were removed. After washing twice with PBS, the pellets were resuspended in Opti-MEM for transduction. To quantify the binding of RNA, the T4-RNP complex was treated with 0.5 μg/μl proteinase K (Fermentas®), 50 mM ethylenediaminetetraacetic acid (EDTA), and 0.2% SDS for 30 min at 65° C. to release the packaged DNA and displayed RNA, followed by agarose gel electrophoresis.

Example 6 T4-AV Assembly

The DNA-packaged and/or protein-displayed T4 nanoparticles as above were diluted in 50 μl of Opti-MEM and mixed gently. Meanwhile, 50 μl Opti-MEM medium was added to a separate sterile tube, followed by addition of an appropriate amount of cationic lipids such as lipofectamine 2000, lipofectamine 3000, lipofectamine RNAiMAX, lipofectamine LTX, lipofectamine stem, and ExpiFectamine® 293 (EXPI) (Thermo Scientific®). After 5 min incubation, the T4 particles were added, gently mixed, and incubated for 20 minutes at room temperature without shaking to allow the formation of T4-AVs. The total volume of the mixture is 100 μl.

Example 7 Cell Culture

HEK293 cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM, Gibco®) supplemented with 10% fetal bovine serum (FBS, Invitrogen®), 1× HEPES (Gibco®), and 1% antibiotics (Gibco®) (complete DMEM). Cells were maintained in a humidified atmosphere at 37° C. and 5% CO₂ and grown until ˜80-90% confluent. Cells were then dissociated from adherent surfaces using 0.05% trypsin/EDTA (Gibco®) and passaged at a subcultivation ratio of 1:5.

Example 8 Cell Transduction

One day prior to transduction, HEK293 cells were transferred to 24-well plates at 2×10⁵ cells per well in complete DMEM. On the day of transduction, the cells were incubated with T4-AVs in antibiotic-free Opti-MEM for 6 h. Thereafter, Opti-MEM was removed and replaced with complete DMEM. The cells were further incubated at 37° C. for an additional 48 h for further analysis. GFP/mCherry transgene expression was observed by fluorescence microscopy (Carl Zeiss®) at 48 h post-transduction, and the average fluorescence intensities were quantified by ImageJ software. The nucleus was counterstained with Hoechst 33342 (Thermo Scientific®) at 37° C. for 20 min.

Example 9 Quantification of Luciferase Activity

To analyze luciferase gene delivery into cells by T4-AVs, luciferase activity was measured with the Luciferase Assay System (Promega®, USA) according to manufacturer's recommended protocol. Briefly, growth medium was removed, and cells were rinsed with PBS buffer. After removing the wash buffer, 150 μl of passive lysis buffer was added to each well, followed by gentle shaking at room temperature for 20 min. Twenty microliters of the cell lysate were then transferred to a 96-well white opaque plate and mixed with 80 μl of Luciferase Assay Reagent, and the luminescence signal was recorded by the Glomax Multi Detection System (Promega®). Triplicate measurements were applied to each group.

Example 10

Beta Galactosidase (β-gal) Transduction

The activity of the Soc-β-gal enzyme delivered by T4-AVs into cells was determined by staining with X-Gal using the β-Galactosidase Staining kit (Sigma®). The representative staining images were captured by ChemiDoc Imaging System (Bio-Rad®).

Example 11 Effect of Endocytosis Inhibitors

Cells were seeded in 24-well plates at 2×10⁵ cells per well in complete DMEM. After 24 h, the cells were pre-incubated in antibiotic-free Opti-MEM for 30 min, with several inhibitors such as sucrose/chlorpromazine for clathrin-mediated endocytosis, methyl-β-cyclodextrin (M-β-CD) for lipid raft, dynasore for dynamin-mediated endocytosis, amiloride for macropinocytosis, nystatin for caveolin-mediated endocytosis, and cytochalasin D for actin cytoskeleton rearrangement. The cells were then exposed to T4-AVs packaged with luciferase or GFP reporter gene for another 6 h in the presence of the inhibitors. Thereafter, Opti-MEM was removed and replaced with complete DMEM. The cells were further incubated at 37° C. for an additional 48 h for luciferase or GFP signal analysis.

Example 12 Cell Proliferation Assay

Cell viability was determined using the CellTiter-Glo® Luminescent Cell Viability Assay Kit (Promega®) after transfection for 48 h following the manufacturer's protocol. Briefly, an equal volume of CellTiter-Glo® Reagent was added to the cell culture in each well. The mixture was horizontally shaken for 2 min to induce cell lysis and then incubated at room temperature for 10 min to stabilize the luminescence signal, which was then recorded by the Glomax® Multi Detection System (Promega®). The viability of the untreated cell group was normalized to 100%, and triplicate measurements were applied to each sample.

Example 13 Western Blotting Analyses

Briefly, the transduced cells were resuspended in loading buffer and boiled for 10 min, separated by 12% SDS-PAGE, and then transferred to nitrocellulose membranes (Bio-Rad®). Blocking was performed in 5% BSA/PBS-T buffer (PBS with 0.05% Tween-20, pH 7.4) at room temperature for 1 h with gentle shaking. Blots were then washed three times with PBS-T. Primary anti-GFP, anti-tubulin, or anti-His6 antibodies were added to the blots and incubated overnight at 4° C. in PBS with 5% BSA. After washing with PBS-T three times, a secondary goat anti-mouse HRP-conjugated antibody (Invitrogen®) was applied at a 1:10,000 dilution in 5% BSA/PBS-T for 1 h at room temperature, followed by rinsing three times with PBS-T. Signals were visualized with an enhanced chemiluminescence substrate (BioRad®, USA) using the BioRad® Gel Doc XR+ system and Image Lab software (BioRad®, USA).

Example 14 Genomic DNA Extraction and T7EI Assay for Genome Modification

HEK293 cells were transfected with various genome editing AVs as described in the present disclosure. Cells were incubated at 37° C. for 72 h post-transduction. Genomic DNA was purified using the GeneJET™ Genomic DNA Purification kit (Thermo Scientific®) following the manufacturer's instructions. Briefly, cells were resuspended in a lysis solution/Proteinase K and incubated at 56° C. for 10 min, followed by the treatment with RNAase A at room temperature for 10 min. GeneJET™ column was used to absorb genomic DNA and washed with wash buffer. Genomic DNA was eluted with elution buffer and stored at −20° C. Genomic region surrounding the AAVS1 or HBB target site was amplified, and PCR products were purified using Qiagen® Mini kit (Qiagen®) following the manufacturer's protocol. A total of 400 ng or 200 ng of the purified PCR products were mixed with 2 μl 10× NEB® buffer 2 (NEB®) and nuclease-free water to a final volume of 20 ∞l, and annealed to enable heteroduplex formation using the following incubations: 95° C. for 10 min, 95° C. to 85° C. ramping at −2° C./s, 85° C. to 25° C. at −0.1° C./s, and 4° C. for hold. T7 Endonuclease I was then added to the annealed PCR product and incubated at 37° C. for 30 min. T7EI digestion product was analyzed on 1.5% (wt/vol) agarose gel. Gels were imaged with a GelDoc® gel imaging system (Bio-Rad®) and quantification was based on relative band intensities using ImageJ software. The estimated gene modification was calculated using the following formula: indel (%)=100×(1−(1−fraction cleaved)^(1/2))³⁶.

Example 15

AAVS1 gRNA In Vitro Synthesis

A DNA template (SEQ ID NO: 1) containing the T7 promoter, the gRNA target and the gRNA scaffold sequences for Cas9 was amplified by PCR with Phusion High-Fidelity PCR Master Mix (Thermo Scientific®). The T7-gRNA PCR fragment was gel-purified and used as a template for in vitro transcription using the HiScribe T7 High Yield RNA Synthesis Kit (NEB®). T7 transcription was performed overnight, and then RNA was purified using the MEGAclear Transcription Clean-Up Kit (Thermo Scientific®). The gRNA was eluted with RNase-free water, analyzed by agarose gel electrophoresis, quantified with Nanodrop® 2000 (Thermo Scientific®), and stored at −80° C.

Example 16 In Vitro CRISPR RNP Binding and Cleavage Assay

To test the binding of Cas9 or Cas9-Soc to gRNA/siRNA/mRNA, the purified protein and RNA at different ratios were incubated at room temperature for 1 h, and then analyzed by agarose gel electrophoresis. The genomic region surrounding the AAVS1 target site was amplified by PCR with Hot-Start DNA Polymerases (Thermo Scientific®), purified by Qiagen® Mini kit (Qiagen®), and used as the substrate for Cas9 cleavage assay. In a reaction volume of 20 μl containing NEB® buffer 3 (100 mM NaCl, 50 mM Tris-HCl, 10 mM MgCl₂, and 1 mM DTT, pH 7.9) and PCR product (300 ng), purified Cas9 or Cas9-Soc (50 nM) and AAVS1gRNA (50 nM) were added. After incubation for 1 h at 37° C., the DNA was analyzed by 1.5% (wt/vol) agarose gel electrophoresis.

Example 17 In Vitro Cre-Hoc Recombination Assay

LSL-GFP plasmid was used as the substrate for testing Cre-Hoc recombination in vitro. In a reaction volume of 50 μl containing recombination buffer (33 mM NaCl, 50 mM Tris-HCl, and 10 mM MgCl₂, pH 7.5) and LSL-GFP plasmid, increasing amounts of purified Cre-Hoc protein were added. After incubation at 37° C. for 30 min and then at 70° C. for 10 minutes, the DNA was analyzed by 0.8% (wt/vol) agarose gel electrophoresis.

Example 18 Enzyme-Linked Immunosorbent Assay (ELISA) for VRCO1 Antibody and CH58 Antibody Quantification

HEK293 cells were transduced with AVs packaged with the linearized plasmids expressing the heavy chain and light chain of VRC01 and/or CH58. After culturing for 3 days, cell culture supernatants were harvested and analyzed for the concentration of antibody by ELISA. ELISA plates (Evergreen Scientific®, 96-well) were coated with 0.1 μg of HIV-1JRFL gp140 envelope protein per well in coating buffer (0.05 M sodium carbonate-sodium bicarbonate, pH 9.6) overnight at 4° C. After washing three times with PBS buffer (pH 7.4), the plates were blocked with PBS-3% BSA buffer for 1 h at 37° C. Known quantities of purified VRCO1 or CH58 monoclonal antibodies in five-fold serial dilution were added to triplicate wells to generate a standard curve, with a starting concentration of 2000 ng mL⁻¹. The concentrations of VRCO1 or CH58 in cell culture medium were determined using a 5-fold dilution series in PBS-1% BSA. The diluted samples were added to each well, and the plates were incubated at 37° C. for 1 h and washed five times with PBS-T buffer (PBS with 0.05% Tween-20, pH 7.4). The secondary goat anti-human IgG-HRP antibody was then added to each well at a 1:5000 dilution and incubated for 1 h at 37° C., followed by washing five times with PBS-T buffer. Next, the TMB (3,3′,5,5′-tetramethylbenzidine) Microwell™ Peroxidase Substrate System (KPL) was applied in the dark for color development. After 10 min, the enzymatic reaction was quenched by adding TMB BlueSTOP™ (KPL) solution, and plates were read within 30 min at 650 nm using an ELISA reader (VERSA Max™, Molecular Devices).

Example 19 Statistics

All quantified data are shown as the mean±standard deviation (SD). Statistical analyses were performed by two-tailed Student's t-tests. The difference between the two groups was considered statistically significant when p<0.05 or highly significant when p<0.01.

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The following references are referred to above and are incorporated herein by reference:

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All documents, patents, journal articles and other materials cited in the present application are incorporated herein by reference.

While the present disclosure has been disclosed with references to certain embodiments, numerous modifications, alterations, and changes to the described embodiments are possible without departing from the sphere and scope of the present disclosure, as defined in the appended claims. Accordingly, it is intended that the present disclosure not be limited to the described embodiments, but that it has the full scope defined by the language of the following claims, and equivalents thereof. 

1. A human genome remodeling artificial virus (AV) comprising: at least one viral vector; at least one therapeutic molecule; and a lipid coating, wherein at least one of the therapeutic molecules has gene modification or gene silencing activities.
 2. The AV of claim 1, wherein the at least one viral vector is selected from the group consisting of Lambda phage, Bacillus phage Phi29, Escherichia coli phages T2, T3, T4 and T7, Enterobacteriaphage P22, phage SPP1, Herpes viruses, adenoviruses, adeno-associated viruses (AAV), retroviruses, lentiviruses.
 3. The AV of claim 1, wherein the at least one therapeutic molecule is selected from the group consisting of DNA, RNA, protein, and complex thereof.
 4. The AV of claim 1, wherein the at least one therapeutic molecule is packaged inside the viral vector.
 5. The AV of claim 1, wherein the at least one therapeutic molecule is displayed outside the viral vector, wherein the therapeutic molecule binds to the viral vector through at least one protein selected from the group consisting of Hoc and Soc.
 6. The AV of claim 5, wherein the therapeutic molecules displayed comprises at least one selected from the group consisting of ribonucleoprotein (RNP) complex, site-specific recombinase Cre, RNA polymerase, and DNA ligase.
 7. The AV of claim 6, wherein the RNP complex comprises Cas9 protein and at least one RNA molecule selected from the group consisting of mRNA, siRNA and gRNA, wherein the Cas9 protein is connected to the T4 capsid through at least one protein selected from the group consisting of Hoc and Soc.
 8. The AV of claim 7, wherein Cas9-Soc comprises a sequence set forth in SEQ ID NO:
 16. 9. The AV of claim 7, wherein a nuclear localization sequence (NLS) is fused to the N-terminus of Cas9 protein.
 10. The AV of claim 6, wherein the RNP complex comprises Cpf1 protein and at least one RNA molecule selected from the group consisting of mRNA, siRNA and gRNA, wherein the Cpf1 protein is connected to the T4 capsid through at least one protein selected from the group consisting of Hoc and Soc.
 11. The AV of claim 10, wherein Cpf1-Soc comprises a sequence set forth in SEQ ID NO:
 17. 12. The AV of claim 1, wherein the lipid coating comprises at least one cationic lipid.
 13. The AV of claim 12, wherein the cationic lipid is at least one selected from the group consisting of Lipofectamine 2000 (LPF2K), LPFRNAiMAX, LPF3K, LPFLTX, LPF Stem-, EXPI and FECT.
 14. The AV of claim 2, wherein the AV comprises at least two viral vectors connected by protein cross bridge.
 15. The AV of claim 14, wherein the protein cross bridge is Soc-biotin-avidin (SBA) or Hoc-BAP-biotin-avidin (HBBA).
 16. A human genome remodeling artificial virus (AV) comprising: a T4 capsid; Cas9 protein; at least one RNA; at least one DNA; and a lipid coating, wherein the DNA is packaged inside the T4 capsid, wherein the RNA is selected from the group consisting of mRNA, siRNA and gRNA, wherein the lipid coating comprises at least one cationic lipid.
 17. The AV of claim 16, wherein the Cas9 protein and RNA form ribonucleoprotein (RNP) complex and wherein the Cas9 protein is connected to the T4 capsid through at least one protein selected from the group consisting of Hoc and Soc.
 18. The AV of claim 17, wherein Cas9-Soc comprises a sequence set forth in SEQ ID NO:
 16. 19. The AV of claim 16, wherein at least one of the Cas9 protein, Cpf1 protein, RNA, Cre, DNA ligase, and RNA polymerase is packaged inside T4 capsid.
 20. The AV of claim 16 further comprising a site-specific recombinase Cre, displayed outside the T4 capsid through at least one protein selected from the group consisting of Hoc and Soc
 21. The AV of claim 20, wherein Cre-Hoc comprises a sequence set forth in SEQ ID NO: 18, and Cre-Soc comprises a sequence set forth in SEQ ID NO:
 22. 22. A method of genome modification comprising: infecting animal cells with an artificial virus (AV), wherein the AV comprises at least one viral vector; at least one therapeutic molecule; and a lipid coating, wherein at least one of the therapeutic molecules has gene modification or gene silencing activities.
 23. (canceled)
 24. (canceled) 